https://pymolwiki.org/api.php?action=feedcontributions&user=Aflaus&feedformat=atomPyMOLWiki - User contributions [en]2024-03-28T14:23:07ZUser contributionsMediaWiki 1.35.7https://pymolwiki.org/index.php?title=MAC_Install&diff=12251MAC Install2015-12-04T23:25:16Z<p>Aflaus: /* Troubleshooting */</p>
<hr />
<div>[[Category:Installation|Mac]]<br />
<br />
__TOC__<br />
<br />
=Installing MacPyMOL=<br />
==Essentials==<br />
The [http://pymol.org/dsc download] is about as straightforward as it gets, and you can install it wherever it makes you happy. You need a 3 button mouse (clickable scroll wheel = middle button). Apple has finally come to its senses and designed a proper, ergonomically pleasant, [http://www.apple.com/mightymouse/ scrollbutton mouse] that works well with pymol and permits horizontal scrolling. Most other mice will also work well.<br />
<br />
== X11 Hybrid ==<br />
<br />
MacPyMOL comes with a native OSX interface which doesn't require X11 ([http://xquartz.macosforge.org/ XQuartz]). However, some features, like the '''Plugin''' menu, are only available in the X11 interface of PyMOL. There are two ways to launch the X11 interface:<br />
# rename '''/Applications/MacPyMOL.app''' to '''/Applications/MacPyMOLX11Hybrid.app'''<br />
# launch the unix executable with the '''-m''' flag: '''/Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL -m'''<br />
<br />
==Warning on Mouse Drivers==<br />
One word of warning: '''Do not install 3rd party drivers''' for multi-button mice if you can avoid it. These often mess with the mapping of the middle button or have other horrific side effects. Fortunately, with OS X, you should not need to.<br />
==Invoking pymol from the unix command line==<br />
The unix executable resides at MacPyMOL.app/Contents/MacOS/MacPyMOL<br />
<br />
I ([[User:Wgscott|Bill Scott]]) wrote a cheezy [http://xanana.ucsc.edu/Library/init/zsh/local-functions/xtal/pymol pymol] shell script (and zsh function) to invoke this on the command line. It uses mdfind to find the executable. I also use [[MacOSX-specific .pymolrc file|this ~/.pymolrc]] file.<br />
<br />
Additional invokation options and further details are discussed under [[Launching_PyMOL#MacOS_X:]]<br />
<br />
==Extras==<br />
You don't need any of these to use MacPyMOL. But you didn't really '''need''' a Mac either. Face it: You need these.<br />
===Stereo===<br />
http://images.apple.com/powermac/images/graphicspymol20051018.jpg<br />
<br />
The [http://www.apple.com/powermac/upgrade.html latest Macs] finally support [http://www.apple.com/powermac/graphics.html stereo in a window]. There is more information in the [[Monitors Hardware Options]] section.<br />
<br />
===Second Monitor===<br />
The trick to getting MacPyMOL to work in stereo on the second monitor is to force it to initially open on that display by providing an appropriate "-X #" (and perhaps -Y #) option on launch. That way the OpenGL context will be created with stereo support.<br />
<source lang="python"><br />
./MacPyMOL.app/Contents/MacOS/MacPyMOL -X -1000<br />
./MacPyMOL.app/Contents/MacOS/MacPyMOL -X -1000 -Y 100<br />
</source><br />
<br />
'''Source:''' ''Warren DeLano; PyMOL Users Archive''<br />
<br />
=PyMOL and Fink=<br />
Fink is a subsystem that was created to bring the full power of Linux open-source to the Darwin (Apple) platform. It is essentially a full working Linux system integrated with the Apple OS. Even X11 applications can be run. To use PyMOL with fink, you will first need to install [http://fink.sourceforge.net/ fink]. This usually takes a while, but is straightforward.<br />
<br />
Once fink is installed, you have two options: (1) use the PyMOL package setup by [[User:wgscott|wgscott]], which might be old, but easier to install; or, download the PyMOL source and build. As usual, it comes down to ease of install vs. new features.<br />
<br />
== PyMOL Directly from Fink ==<br />
To install PyMOL directly from fink, type:<br />
<source lang="bash"><br />
fink install pymol-py27<br />
</source><br />
<br />
This will install python2.7 in fink, along with an X-windows based tkinter. There are also versions that permit you to install PyMOL to interact with python2.6 and older (as of Mar-12-2013). Fink uses its own unix-type python installation. For other versions list up pymol packages using '''fink list pymol*''' on command line.<br />
<br />
===Notes and Possible Issues ===<br />
* The [http://pdb.finkproject.org/pdb/package.php/pymol-py25 fink pymol package] currently exists in the [http://fink.sourceforge.net/faq/usage-fink.php#unstable unstable branch of fink], so you will either have to [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/How_to_Activate_the_Unstable_Branch activate the unstable branch] or make the following symbolic links:<br />
<source lang="bash"><br />
sudo ln -s /sw/fink/dists/unstable/main/finkinfo/sci/pymol-py.* /sw/fink/dists/local/main/finkinfo/.<br />
</source> <br />
You might need to create the latter directory if it doesn't already exist, i.e., issue the command<br />
<source lang="bash"><br />
sudo mkdir -p /sw/fink/dists/local/main/finkinfo<br />
</source><br />
* 10.4 ONLY: Be sure to set your display environment in your start up shell script to use pymol. For example in your home directory, the .bashrc (or .bash_profile) file should contain:<br />
<source lang="bash"><br />
export DISPLAY=":0.0"<br />
</source><br />
Do NOT set the DISPLAY variable for 10.5+, as God does this for you automatically. If for some reason you don't want to set DISPLAY, launch X11 manually (Applications/Utilities) then start a login shell with 'xterm -ls' (note default xterm is not a login shell so will not read .bashrc) and finally issue 'pymol' <br />
* Fink pymol also reads ~/.pymolrc in your home directory.<br />
* I ([[User:wgscott|wgscott]]) have put a whole lot of further information on how to use fink to install crystallographic software on my own [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Main_Page wiki] and [http://chemistry.ucsc.edu/~wgscott/xtal/ website], including instructions on [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Getting_your_fink_installation_to_use_packages_that_I_have_pre-compiled how to install precompiled binary packages using fink].<br />
<br />
* The [http://pdb.finkproject.org/pdb/search.php?summary=pymol fink pymol package] is currently maintained by Jack Howarth.<br />
<br />
= PyMOL Install from Source, Using Fink =<br />
If the above didn't work, or you really want the latest PyMOL code, then:<br />
* Download the latest PyMOL source and unpack it.<br />
* Ensure that you have installed, in Fink:<br />
** python-2.5 pmw-py25<br />
** mesa mesa-shlibs<br />
** libpng3 libpng3-shlibs<br />
** freetype2 freetype2-deve<br />
** freeglut freeglut-shlibs<br />
* Change directory into the new PyMOL dir, eg. ''cd pymol''<br />
* Then, install PyMOL with,<br />
<source lang="bash"><br />
/sw/bin/python setup.py install<br />
</source><br />
<br />
==Notes and Possible Issues==<br />
* If you get an error about '''-Wno-long-double''' then your gcc is mismatched. I fixed this by pointing the symbolic link ''/usr/bin/gcc'' from ''/usr/bin/gcc-4.2'' to ''/usr/bin/gcc-4.0''. Or, in code,<br />
<source lang="bash"><br />
# These command are commented out to stop people from copy/pasting b/c <br />
# these are possibly dangerous for your system. Ensure that /usr/bin/gcc<br />
# is a symbolic link and not a real binary. If so, I used the following<br />
# to fix the -Wno-long-double error.<br />
# sudo rm /usr/bin/gcc<br />
# sudo ln -s /usr/bin/gcc-4.0 /usr/bin/gcc<br />
</source><br />
* If you get an error about something like ''GL_PALETTE_TEXTURE'' then you need to comment out those few lines in the code that throws the error. Read the output.<br />
<br />
==Install APBS with Fink==<br />
<br />
To use the electrostatics plugin, you will need [http://apbs.sourceforge.net/ APBS] and its dependencies. These are also available as Fink packages, and include [http://pdb.finkproject.org/pdb/package.php/apbs APBS], [http://pdb.finkproject.org/pdb/package.php/maloc maloc] and [http://pdb.finkproject.org/pdb/package.php/pdb2pqr pdb2pqr]. If you have multiple processors available, you might wish to install the [http://pdb.finkproject.org/pdb/package.php/apbs-mpi-openmpi MPI version of APBS].<br />
<br />
Issuing the command<br />
<br />
fink install apbs<br />
<br />
will install apbs and its required dependencies for you. The fink pymol package is already preconfigured to do the right thing to use apbs as a plugin.<br />
<br />
=PyMOL in MacPorts=<br />
Recent versions of [http://www.macports.org/ MacPorts] include a hybrid PyMOL. It can be installed with:<br />
sudo port install pymol<br />
<br />
Make sure that the Tk and Tcl packages are installed with the required flags:<br />
sudo port -f uninstall tcl<br />
sudo port -f uninstall tk<br />
<br />
sudo port install tcl -corefoundation<br />
sudo port install tk -quartz<br />
<br />
==Troubleshooting==<br />
; When selecting atoms with the mouse, no matter how well one aims, the atoms selected are actually those far from the ones wanted: This is a known problem. Select "Millions of Colors" in '''System Preferences->Display'''.<br />
; There seems to be a race condition between the Tk window and the openGL window. (The focus for the windows are very quickly flashing back and forth.): This is a well-known problem. The blame here is circular: Apple blames developers, developers blame Apple. Regardless, it appears to have been fixed with the latest Mac OS X (10.6) release. Upgrade to 10.6 and this problem goes away.<br />
;When using multiple displays, the OpenGL window flickers; moving the window between displays crashes the whole session [https://trac.macports.org/ticket/24895]: If you don't need stereo then start PyMOL in mono mode with <pre>pymol -M</pre>If you need stereo then you probably need to wait for a fix in the graphics driver.<br />
<br />
=Installing PyMOL with Homebrew=<br />
== General Procedure ==<br />
====1. Install [http://brew.sh/ homebrew].====<br />
At a Terminal prompt, copy and paste the following command and follow the on-screen instructions.<br />
<nowiki>ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"</nowiki><br />
You will be prompted to install the the Xcode Command Line Tools if you don't already have them. After installation finishes, it is probably a good idea to run<br />
brew doctor<br />
to make sure there are no issues with your setup.<br />
<br />
====2. Install Xquartz.====<br />
Tcl/Tk requires X11, but since 10.7, Mac OS X no longer comes with X11 by default. Download and install [http://xquartz.macosforge.org Xquartz] to satisfy this requirement. This can also be done with [https://github.com/caskroom/homebrew-cask Homebrew Cask]:<br />
<br />
brew install caskroom/cask/brew-cask<br />
brew cask install xquartz<br />
<br />
====3. Install PyMOL.====<br />
brew install homebrew/science/pymol<br />
You should now have a working PyMOL installation, and be able to launch the program in a Terminal window from any directory with the command <code>pymol</code>.<br />
<br />
=====Troubleshooting=====<br />
If you get this error<br />
Traceback (most recent call last):<br />
File "/usr/local/Cellar/pymol/1.7.4.0/libexec/lib/python2.7/site-packages/pymol/__init__.py", line 71, in <module><br />
import pymol<br />
File "/usr/local/Cellar/pymol/1.7.4.0/libexec/lib/python2.7/site-packages/pymol/__init__.py", line 533, in <module><br />
import pymol._cmd<br />
ImportError: dlopen(/usr/local/Cellar/pymol/1.7.4.0/libexec/lib/python2.7/site-packages/pymol/_cmd.so, 2): Library not loaded: /usr/local/lib/libGLEW.1.11.0.dylib<br />
Referenced from: /usr/local/Cellar/pymol/1.7.4.0/libexec/lib/python2.7/site-packages/pymol/_cmd.so<br />
Reason: image not found<br />
You could try this, linking another libGLEW library to the one who is asked for<br />
ln -s /usr/local/lib/libGLEW.1.12.0.dylib /usr/local/lib/libGLEW.1.11.0.dylib<br />
If you are not sure which version of glew you have:<br />
brew info glew<br />
<br />
== Stereo issues ==<br />
Some older Macs seem to crash with stereo graphics. If this happens to you, a workaround is to launch PyMOL explicitly in Mono mode with `pymol -M`. You can also set up an alias in your ~/.profile:<br />
<br />
alias pymol='pymol -M'<br />
<br />
== With previously brew-installed python or tcl/tk ==<br />
Brewed PyMOL requires python compiled with the --with-tcl-tk option and tcl-tk compiled with the --with-threads and --with-x11 options. If you've already brew-installed either of these packages without these options, you'll have to uninstall and reinstall them as follows, then proceed to install PyMOL (assuming you've already either attempted to `brew install homebrew/science/pymol` or run `brew tap homebrew/science`).<br />
<br />
brew update # just to keep things current<br />
brew uninstall python<br />
brew uninstall tcl-tk<br />
brew install tcl-tk --with-threads --with-x11<br />
brew install python --with-tcl-tk<br />
brew install pymol<br />
<br />
=Miscellaneous installation=<br />
===Exporting MPG movies===<br />
See [[MovieSchool_6#Exporting_your_Movie|MovieSchool 6]] for freemol installation.<BR><br />
<br />
[[Category:Nucleic_Acids|MAC Install]]<br />
[[Category:Technical Issues|MAC Install]]<br />
[[Category:Mac|MAC Install]]</div>Aflaushttps://pymolwiki.org/index.php?title=MAC_Install&diff=8655MAC Install2010-11-14T20:23:57Z<p>Aflaus: clarfy no_tkinter explanation</p>
<hr />
<div>[[Category:Installation|Mac]]<br />
<br />
__TOC__<br />
<br />
=Installing MacPyMOL=<br />
===Essentials===<br />
The [http://pymol.org/dsc download] is about as straightforward as it gets, and you can install it wherever it makes you happy. You need a 3 button mouse (clickable scroll wheel = middle button). Apple has finally come to its senses and designed a proper, ergonomically pleasant, [http://www.apple.com/mightymouse/ scrollbutton mouse] that works well with pymol and permits horizontal scrolling. Most other mice will also work well.<br />
<br />
===Warning on Mouse Drivers===<br />
<br />
One word of warning: '''Do not install 3rd party drivers''' for multi-button mice if you can avoid it. These often mess with the mapping of the middle button or have other horrific side effects. Fortunately, with OS X, you should not need to.<br />
<br />
===Invoking pymol from the unix command line===<br />
<br />
The unix executable resides at MacPyMOL.app/Contents/MacOS/MacPyMOL<br />
<br />
I ([[User:Wgscott|Bill Scott]]) wrote a cheezy [http://xanana.ucsc.edu/Library/init/zsh/local-functions/xtal/pymol pymol] shell script (and zsh function) to invoke this on the command line. It uses mdfind to find the executable. I also use [[MacOSX-specific .pymolrc file|this ~/.pymolrc]] file.<br />
<br />
Additional invokation options and further details are discussed under [[Launching_PyMOL#MacOS_X:]]<br />
<br />
===Extras===<br />
<br />
You don't need any of these to use MacPyMOL. But you didn't really '''need''' a Mac either. Face it: You need these.<br />
<br />
====Mighty Mouse====<br />
<br />
http://images.apple.com/mightymouse/images/index360scroll220050802.gif<br />
<br />
A 3-button mouse is essential. [http://www.apple.com/mightymouse/ Apple's Mighty Mouse] is an extra treat.<br />
<br />
The Mighty Mouse was superseded in late 2009 by the [http://en.wikipedia.org/wiki/Magic_Mouse Magic Mouse]. Although a great mouse with scrolling capability, the magic mouse is a 2-button mouse with gesture-enabled surface, and so lacks a middle button. To use it choose a 2 button mode in the Mouse menu.<br />
<br />
====PowerMate Dial====<br />
<br />
http://www.griffintechnology.com/assets/images/products/powermate/prod_powermate_sub01b.jpg<br />
<br />
The [http://www.chemistry.ucsc.edu/~wgscott/xtal/powermate_pymol_osx.html PowerMate dial works nicely with pymol].<br />
<br />
====Stereo====<br />
<br />
http://images.apple.com/powermac/images/graphicspymol20051018.jpg<br />
<br />
The [http://www.apple.com/powermac/upgrade.html latest Macs] finally support [http://www.apple.com/powermac/graphics.html stereo in a window]. There is more information in the [[Monitors Hardware Options]] section.<br />
<br />
====Second Monitor====<br />
The trick to getting MacPyMOL to work in stereo on the second monitor is to force it to initially open on that display by providing an appropriate "-X #" (and perhaps -Y #) option on launch. That way the OpenGL context will be created with stereo support.<br />
<source lang="python"><br />
./MacPyMOL.app/Contents/MacOS/MacPyMOL -X -1000<br />
./MacPyMOL.app/Contents/MacOS/MacPyMOL -X -1000 -Y 100<br />
</source><br />
<br />
'''Source:''' ''Warren DeLano; PyMOL Users Archive''<br />
<br />
=Installing X-windows based pymol on Mac OS X=<br />
<br />
===Why would you want to do this?===<br />
<br />
#You want to run a [http://www.oreilly.com/openbook/freedom/ free], guilt-free, open-source version of pymol<br />
#You just happen to prefer the [http://wiki.python.org/moin/TkInter tkinter] menu<br />
#You want to use [http://pymol.sourceforge.net/plugins.html plugins], for example, the [http://www-personal.umich.edu/~mlerner/PyMOL/ apbs plugin] for free grasp-like electrostatic calculations.<br />
<br />
----<br />
<br />
===PyMOL and Fink===<br />
Fink is a subsystem that was created to bring the full power of Linux open-source to the Darwin (Apple) platform. It is essentially a full working Linux system integrated with the Apple OS. Even X11 applications can be run. To use PyMOL with fink, you will first need to install [http://fink.sourceforge.net/ fink]. This usually takes a while, but is straightforward.<br />
<br />
Once fink is installed, you have two options: (1) use the PyMOL package setup by [[User:wgscott|wgscott]], which might be old, but easier to install; or, download the PyMOL source and build. As usual, it comes down to ease of install vs. new features.<br />
<br />
==== PyMOL Directly from Fink ====<br />
To install PyMOL directly from fink, type:<br />
<source lang="bash"><br />
fink install pymol-py25<br />
</source><br />
<br />
This will install python2.5 in fink, along with an X-windows based tkinter. There are also versions that permit you to install PyMOL to interact with python2.4 and even python2.3. Fink uses its own unix-type python installation.<br />
<br />
=====Notes and Possible Issues =====<br />
* The [http://pdb.finkproject.org/pdb/package.php/pymol-py25 fink pymol package] currently exists in the [http://fink.sourceforge.net/faq/usage-fink.php#unstable unstable branch of fink], so you will either have to [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/How_to_Activate_the_Unstable_Branch activate the unstable branch] or make the following symbolic links:<br />
<source lang="bash"><br />
sudo ln -s /sw/fink/dists/unstable/main/finkinfo/sci/pymol-py.* /sw/fink/dists/local/main/finkinfo/.<br />
</source> <br />
You might need to create the latter directory if it doesn't already exist, i.e., issue the command<br />
<source lang="bash"><br />
sudo mkdir -p /sw/fink/dists/local/main/finkinfo<br />
</source><br />
* 10.4 ONLY: Be sure to set your display environment in your start up shell script to use pymol. For example in your home directory, the .bashrc (or .bash_profile) file should contain:<br />
<source lang="bash"><br />
export DISPLAY=":0.0"<br />
</source><br />
Do NOT set the DISPLAY variable for 10.5+, as God does this for you automatically. If for some reason you don't want to set DISPLAY, launch X11 manually (Applications/Utilities) then start a login shell with 'xterm -ls' (note default xterm is not a login shell so will not read .bashrc) and finally issue 'pymol' <br />
* Fink pymol also reads ~/.pymolrc in your home directory.<br />
* I ([[User:wgscott|wgscott]]) have put a whole lot of further information on how to use fink to install crystallographic software on my own [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Main_Page wiki] and [http://chemistry.ucsc.edu/~wgscott/xtal/ website], including instructions on [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Getting_your_fink_installation_to_use_packages_that_I_have_pre-compiled how to install precompiled binary packages using fink].<br />
<br />
* The [http://pdb.finkproject.org/pdb/search.php?summary=pymol fink pymol package] is currently maintained by Jack Howarth.<br />
<br />
<br />
<br />
==== PyMOL Install from Source, Using Fink ====<br />
If the above didn't work, of you really want the latest PyMOL code, then<br />
* Download the latest PyMOL source and unpack it.<br />
* Ensure that you have installed, in Fink:<br />
** python-2.5 pmw-py25<br />
** mesa mesa-shlibs<br />
** libpng3 libpng3-shlibs<br />
** freetype2 freetype2-deve<br />
** freeglut freeglut-shlibs<br />
* Change directory into the new PyMOL dir, eg. ''cd pymol''<br />
* Then, install PyMOL with,<br />
<source lang="bash"><br />
/sw/bin/python setup.py install<br />
</source><br />
<br />
=====Notes and Possible Issues=====<br />
* If you get an error about '''-Wno-long-double''' then your gcc is mismatched. I fixed this by pointing the symbolic link ''/usr/bin/gcc'' from ''/usr/bin/gcc-4.2'' to ''/usr/bin/gcc-4.0''. Or, in code,<br />
<source lang="bash"><br />
# These command are commented out to stop people from copy/pasting b/c <br />
# these are possibly dangerous for your system. Ensure that /usr/bin/gcc<br />
# is a symbolic link and not a real binary. If so, I used the following<br />
# to fix the -Wno-long-double error.<br />
# sudo rm /usr/bin/gcc<br />
# sudo ln -s /usr/bin/gcc-4.0 /usr/bin/gcc<br />
</source><br />
* If you get an error about something like ''GL_PALETTE_TEXTURE'' then you need to comment out those few lines in the code that throws the error. Read the output.<br />
<br />
====Install APBS and friends with fink====<br />
<br />
[[Image:Rna_surface_apbs.png|thumb|APBS calculated electrostatic potential of SARS s2m RNA reveals the colors of a true patriot.]]<br />
<br />
To use the electrostatics plugin, you will need [http://apbs.sourceforge.net/ APBS] and its dependencies. These are also available as fink packages, and include [http://pdb.finkproject.org/pdb/package.php/apbs apbs], [http://pdb.finkproject.org/pdb/package.php/maloc maloc] and [http://pdb.finkproject.org/pdb/package.php/pdb2pqr pdb2pqr]. If you have multiple processors available, you might wish to install the [http://pdb.finkproject.org/pdb/package.php/apbs-mpi-openmpi mpi version of apbs].<br />
<br />
Issuing the command<br />
<br />
fink install apbs<br />
<br />
will install apbs and its required dependencies for you. The fink pymol package is already preconfigured to do the right thing to use apbs as a plugin. Here is [http://xanana.ucsc.edu/xtal/pymol_screenshot.png a big screenshot of the fink APBS package being invoked via the pymol plugin].<br />
<br />
'''Nucleic acids''' may prove problematic for the apbs plugin. If so, use the pdb2pqr command-line tool to create a pqr file manually, instead of using the plugin to generate it.<br />
<br />
----<br />
<br />
===PyMOLX11Hybrid=== <br />
<br />
MacPyMOL for Tiger now includes a hybrid X11 mode. Assuming that X11 is already installed, simply duplicate MacPyMOL.app and rename it "PyMOLX11Hybrid.app" and launch.<br />
<br />
<br />
===PyMOL in MacPorts===<br />
<br />
Recent versions of [http://www.macports.org/ MacPorts] (at least 1.8.2) also include a hybrid PyMOL and also apbs. One can install it with<br />
sudo port install pymol apbs apbs-mpi<br />
<br />
====Pymol from MacPorts using simple GUI approach====<br />
<br />
# Install [http://guide.macports.org/#installing MacPorts], including Xcode Tools and X11 if necessary<br />
# Install a MacPorts [http://trac.macports.org/wiki/FAQ#gui GUI client], for example [http://porticus.alittledrop.com/ Porticus]. Do a Selfupdate.<br />
# Search for Pymol via gui and install<br />
# Launch Terminal app and execute pymol<br />
<br />
=====Config issues=====<br />
<br />
* If you already have a .bash_profile, you may need to copy the lines which macports [http://guide.macports.org/#installing.shell installation puts in .profile] into .bash_profile<br />
* Pymol installation in macports uses the subversion repository so you may need to configure the svn command line client [http://svnbook.red-bean.com/en/1.1/ch07.html#svn-ch-7-sect-1.3.1 config file] for your proxy settings in ~/.subversion/servers<br />
* If the menu/control window does not appear when launching pymol and the terminal window reports "ImportError: No module named _tkinter", macports python may have installed without tkinter even if the no_tkinter option was not selected in the gui. To fix, uninstall python26 via gui then execute the following at the command line to force ignoring of no_tkinter.<br />
<br />
sudo port install python26 -no_tkinter<br />
<br />
===Troubleshooting===<br />
<br />
; When selecting atoms with the mouse, no matter how well one aims, the atoms selected are actually those far from the ones wanted: This is a known problem. Select "Millions of Colors" in '''System Preferences->Display'''.<br />
; There seems to be a race condition between the Tk window and the openGL window. (The focus for the windows are very quickly flashing back and forth.): This is a well-known problem. The blame here is circular: Apple blames developers, developers blame Apple. Regardless, it appears to have been fixed with the latest Mac OS X (10.6) release. Upgrade to 10.6 and this problem goes away.<br />
;When using multiple displays, the OpenGL window flickers; moving the window between displays crashes the whole session [https://trac.macports.org/ticket/24895]: If you don't need stereo then start PyMOL in mono mode with <pre>pymol -M</pre>If you need stereo then you probably need to wait for a fix in the graphics driver.<br />
<br />
<br />
<br />
<br />
<br />
<br />
[[Category:Nucleic_Acids|MAC Install]]<br />
[[Category:Technical Issues|MAC Install]]</div>Aflaushttps://pymolwiki.org/index.php?title=MAC_Install&diff=8654MAC Install2010-11-14T20:20:28Z<p>Aflaus: /* Pymol with MacPorts via Simple GUI */</p>
<hr />
<div>[[Category:Installation|Mac]]<br />
<br />
__TOC__<br />
<br />
=Installing MacPyMOL=<br />
===Essentials===<br />
The [http://pymol.org/dsc download] is about as straightforward as it gets, and you can install it wherever it makes you happy. You need a 3 button mouse (clickable scroll wheel = middle button). Apple has finally come to its senses and designed a proper, ergonomically pleasant, [http://www.apple.com/mightymouse/ scrollbutton mouse] that works well with pymol and permits horizontal scrolling. Most other mice will also work well.<br />
<br />
===Warning on Mouse Drivers===<br />
<br />
One word of warning: '''Do not install 3rd party drivers''' for multi-button mice if you can avoid it. These often mess with the mapping of the middle button or have other horrific side effects. Fortunately, with OS X, you should not need to.<br />
<br />
===Invoking pymol from the unix command line===<br />
<br />
The unix executable resides at MacPyMOL.app/Contents/MacOS/MacPyMOL<br />
<br />
I ([[User:Wgscott|Bill Scott]]) wrote a cheezy [http://xanana.ucsc.edu/Library/init/zsh/local-functions/xtal/pymol pymol] shell script (and zsh function) to invoke this on the command line. It uses mdfind to find the executable. I also use [[MacOSX-specific .pymolrc file|this ~/.pymolrc]] file.<br />
<br />
Additional invokation options and further details are discussed under [[Launching_PyMOL#MacOS_X:]]<br />
<br />
===Extras===<br />
<br />
You don't need any of these to use MacPyMOL. But you didn't really '''need''' a Mac either. Face it: You need these.<br />
<br />
====Mighty Mouse====<br />
<br />
http://images.apple.com/mightymouse/images/index360scroll220050802.gif<br />
<br />
A 3-button mouse is essential. [http://www.apple.com/mightymouse/ Apple's Mighty Mouse] is an extra treat.<br />
<br />
The Mighty Mouse was superseded in late 2009 by the [http://en.wikipedia.org/wiki/Magic_Mouse Magic Mouse]. Although a great mouse with scrolling capability, the magic mouse is a 2-button mouse with gesture-enabled surface, and so lacks a middle button. To use it choose a 2 button mode in the Mouse menu.<br />
<br />
====PowerMate Dial====<br />
<br />
http://www.griffintechnology.com/assets/images/products/powermate/prod_powermate_sub01b.jpg<br />
<br />
The [http://www.chemistry.ucsc.edu/~wgscott/xtal/powermate_pymol_osx.html PowerMate dial works nicely with pymol].<br />
<br />
====Stereo====<br />
<br />
http://images.apple.com/powermac/images/graphicspymol20051018.jpg<br />
<br />
The [http://www.apple.com/powermac/upgrade.html latest Macs] finally support [http://www.apple.com/powermac/graphics.html stereo in a window]. There is more information in the [[Monitors Hardware Options]] section.<br />
<br />
====Second Monitor====<br />
The trick to getting MacPyMOL to work in stereo on the second monitor is to force it to initially open on that display by providing an appropriate "-X #" (and perhaps -Y #) option on launch. That way the OpenGL context will be created with stereo support.<br />
<source lang="python"><br />
./MacPyMOL.app/Contents/MacOS/MacPyMOL -X -1000<br />
./MacPyMOL.app/Contents/MacOS/MacPyMOL -X -1000 -Y 100<br />
</source><br />
<br />
'''Source:''' ''Warren DeLano; PyMOL Users Archive''<br />
<br />
=Installing X-windows based pymol on Mac OS X=<br />
<br />
===Why would you want to do this?===<br />
<br />
#You want to run a [http://www.oreilly.com/openbook/freedom/ free], guilt-free, open-source version of pymol<br />
#You just happen to prefer the [http://wiki.python.org/moin/TkInter tkinter] menu<br />
#You want to use [http://pymol.sourceforge.net/plugins.html plugins], for example, the [http://www-personal.umich.edu/~mlerner/PyMOL/ apbs plugin] for free grasp-like electrostatic calculations.<br />
<br />
----<br />
<br />
===PyMOL and Fink===<br />
Fink is a subsystem that was created to bring the full power of Linux open-source to the Darwin (Apple) platform. It is essentially a full working Linux system integrated with the Apple OS. Even X11 applications can be run. To use PyMOL with fink, you will first need to install [http://fink.sourceforge.net/ fink]. This usually takes a while, but is straightforward.<br />
<br />
Once fink is installed, you have two options: (1) use the PyMOL package setup by [[User:wgscott|wgscott]], which might be old, but easier to install; or, download the PyMOL source and build. As usual, it comes down to ease of install vs. new features.<br />
<br />
==== PyMOL Directly from Fink ====<br />
To install PyMOL directly from fink, type:<br />
<source lang="bash"><br />
fink install pymol-py25<br />
</source><br />
<br />
This will install python2.5 in fink, along with an X-windows based tkinter. There are also versions that permit you to install PyMOL to interact with python2.4 and even python2.3. Fink uses its own unix-type python installation.<br />
<br />
=====Notes and Possible Issues =====<br />
* The [http://pdb.finkproject.org/pdb/package.php/pymol-py25 fink pymol package] currently exists in the [http://fink.sourceforge.net/faq/usage-fink.php#unstable unstable branch of fink], so you will either have to [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/How_to_Activate_the_Unstable_Branch activate the unstable branch] or make the following symbolic links:<br />
<source lang="bash"><br />
sudo ln -s /sw/fink/dists/unstable/main/finkinfo/sci/pymol-py.* /sw/fink/dists/local/main/finkinfo/.<br />
</source> <br />
You might need to create the latter directory if it doesn't already exist, i.e., issue the command<br />
<source lang="bash"><br />
sudo mkdir -p /sw/fink/dists/local/main/finkinfo<br />
</source><br />
* 10.4 ONLY: Be sure to set your display environment in your start up shell script to use pymol. For example in your home directory, the .bashrc (or .bash_profile) file should contain:<br />
<source lang="bash"><br />
export DISPLAY=":0.0"<br />
</source><br />
Do NOT set the DISPLAY variable for 10.5+, as God does this for you automatically. If for some reason you don't want to set DISPLAY, launch X11 manually (Applications/Utilities) then start a login shell with 'xterm -ls' (note default xterm is not a login shell so will not read .bashrc) and finally issue 'pymol' <br />
* Fink pymol also reads ~/.pymolrc in your home directory.<br />
* I ([[User:wgscott|wgscott]]) have put a whole lot of further information on how to use fink to install crystallographic software on my own [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Main_Page wiki] and [http://chemistry.ucsc.edu/~wgscott/xtal/ website], including instructions on [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Getting_your_fink_installation_to_use_packages_that_I_have_pre-compiled how to install precompiled binary packages using fink].<br />
<br />
* The [http://pdb.finkproject.org/pdb/search.php?summary=pymol fink pymol package] is currently maintained by Jack Howarth.<br />
<br />
<br />
<br />
==== PyMOL Install from Source, Using Fink ====<br />
If the above didn't work, of you really want the latest PyMOL code, then<br />
* Download the latest PyMOL source and unpack it.<br />
* Ensure that you have installed, in Fink:<br />
** python-2.5 pmw-py25<br />
** mesa mesa-shlibs<br />
** libpng3 libpng3-shlibs<br />
** freetype2 freetype2-deve<br />
** freeglut freeglut-shlibs<br />
* Change directory into the new PyMOL dir, eg. ''cd pymol''<br />
* Then, install PyMOL with,<br />
<source lang="bash"><br />
/sw/bin/python setup.py install<br />
</source><br />
<br />
=====Notes and Possible Issues=====<br />
* If you get an error about '''-Wno-long-double''' then your gcc is mismatched. I fixed this by pointing the symbolic link ''/usr/bin/gcc'' from ''/usr/bin/gcc-4.2'' to ''/usr/bin/gcc-4.0''. Or, in code,<br />
<source lang="bash"><br />
# These command are commented out to stop people from copy/pasting b/c <br />
# these are possibly dangerous for your system. Ensure that /usr/bin/gcc<br />
# is a symbolic link and not a real binary. If so, I used the following<br />
# to fix the -Wno-long-double error.<br />
# sudo rm /usr/bin/gcc<br />
# sudo ln -s /usr/bin/gcc-4.0 /usr/bin/gcc<br />
</source><br />
* If you get an error about something like ''GL_PALETTE_TEXTURE'' then you need to comment out those few lines in the code that throws the error. Read the output.<br />
<br />
====Install APBS and friends with fink====<br />
<br />
[[Image:Rna_surface_apbs.png|thumb|APBS calculated electrostatic potential of SARS s2m RNA reveals the colors of a true patriot.]]<br />
<br />
To use the electrostatics plugin, you will need [http://apbs.sourceforge.net/ APBS] and its dependencies. These are also available as fink packages, and include [http://pdb.finkproject.org/pdb/package.php/apbs apbs], [http://pdb.finkproject.org/pdb/package.php/maloc maloc] and [http://pdb.finkproject.org/pdb/package.php/pdb2pqr pdb2pqr]. If you have multiple processors available, you might wish to install the [http://pdb.finkproject.org/pdb/package.php/apbs-mpi-openmpi mpi version of apbs].<br />
<br />
Issuing the command<br />
<br />
fink install apbs<br />
<br />
will install apbs and its required dependencies for you. The fink pymol package is already preconfigured to do the right thing to use apbs as a plugin. Here is [http://xanana.ucsc.edu/xtal/pymol_screenshot.png a big screenshot of the fink APBS package being invoked via the pymol plugin].<br />
<br />
'''Nucleic acids''' may prove problematic for the apbs plugin. If so, use the pdb2pqr command-line tool to create a pqr file manually, instead of using the plugin to generate it.<br />
<br />
----<br />
<br />
===PyMOLX11Hybrid=== <br />
<br />
MacPyMOL for Tiger now includes a hybrid X11 mode. Assuming that X11 is already installed, simply duplicate MacPyMOL.app and rename it "PyMOLX11Hybrid.app" and launch.<br />
<br />
<br />
===PyMOL in MacPorts===<br />
<br />
Recent versions of [http://www.macports.org/ MacPorts] (at least 1.8.2) also include a hybrid PyMOL and also apbs. One can install it with<br />
sudo port install pymol apbs apbs-mpi<br />
<br />
====Pymol from MacPorts using simple GUI approach====<br />
<br />
# Install [http://guide.macports.org/#installing MacPorts], including Xcode Tools and X11 if necessary<br />
# Install a MacPorts [http://trac.macports.org/wiki/FAQ#gui GUI client], for example [http://porticus.alittledrop.com/ Porticus]. Do a Selfupdate.<br />
# Search for Pymol via gui and install<br />
# Launch Terminal app and execute pymol<br />
<br />
=====Config issues=====<br />
<br />
* If you already have a .bash_profile, you may need to copy the lines which macports [http://guide.macports.org/#installing.shell installation puts in .profile] into .bash_profile<br />
* Pymol installation in macports uses the subversion repository so you may need to configure the svn command line client [http://svnbook.red-bean.com/en/1.1/ch07.html#svn-ch-7-sect-1.3.1 config file] for your proxy settings in ~/.subversion/servers<br />
* If the menu/control window does not appear when launching pymol and the terminal window reports "ImportError: No module named _tkinter" then force uninstall python26 from macports. Execute the following at the command line to force ignoring on no_tkinter. Python may have installed without tkinter, even though the no_tkinter option was not selected in the gui.<br />
<br />
sudo port install python26 -no_tkinter<br />
<br />
===Troubleshooting===<br />
<br />
; When selecting atoms with the mouse, no matter how well one aims, the atoms selected are actually those far from the ones wanted: This is a known problem. Select "Millions of Colors" in '''System Preferences->Display'''.<br />
; There seems to be a race condition between the Tk window and the openGL window. (The focus for the windows are very quickly flashing back and forth.): This is a well-known problem. The blame here is circular: Apple blames developers, developers blame Apple. Regardless, it appears to have been fixed with the latest Mac OS X (10.6) release. Upgrade to 10.6 and this problem goes away.<br />
;When using multiple displays, the OpenGL window flickers; moving the window between displays crashes the whole session [https://trac.macports.org/ticket/24895]: If you don't need stereo then start PyMOL in mono mode with <pre>pymol -M</pre>If you need stereo then you probably need to wait for a fix in the graphics driver.<br />
<br />
<br />
<br />
<br />
<br />
<br />
[[Category:Nucleic_Acids|MAC Install]]<br />
[[Category:Technical Issues|MAC Install]]</div>Aflaushttps://pymolwiki.org/index.php?title=MAC_Install&diff=8653MAC Install2010-11-14T20:19:27Z<p>Aflaus: force python to install with tkinter in macports</p>
<hr />
<div>[[Category:Installation|Mac]]<br />
<br />
__TOC__<br />
<br />
=Installing MacPyMOL=<br />
===Essentials===<br />
The [http://pymol.org/dsc download] is about as straightforward as it gets, and you can install it wherever it makes you happy. You need a 3 button mouse (clickable scroll wheel = middle button). Apple has finally come to its senses and designed a proper, ergonomically pleasant, [http://www.apple.com/mightymouse/ scrollbutton mouse] that works well with pymol and permits horizontal scrolling. Most other mice will also work well.<br />
<br />
===Warning on Mouse Drivers===<br />
<br />
One word of warning: '''Do not install 3rd party drivers''' for multi-button mice if you can avoid it. These often mess with the mapping of the middle button or have other horrific side effects. Fortunately, with OS X, you should not need to.<br />
<br />
===Invoking pymol from the unix command line===<br />
<br />
The unix executable resides at MacPyMOL.app/Contents/MacOS/MacPyMOL<br />
<br />
I ([[User:Wgscott|Bill Scott]]) wrote a cheezy [http://xanana.ucsc.edu/Library/init/zsh/local-functions/xtal/pymol pymol] shell script (and zsh function) to invoke this on the command line. It uses mdfind to find the executable. I also use [[MacOSX-specific .pymolrc file|this ~/.pymolrc]] file.<br />
<br />
Additional invokation options and further details are discussed under [[Launching_PyMOL#MacOS_X:]]<br />
<br />
===Extras===<br />
<br />
You don't need any of these to use MacPyMOL. But you didn't really '''need''' a Mac either. Face it: You need these.<br />
<br />
====Mighty Mouse====<br />
<br />
http://images.apple.com/mightymouse/images/index360scroll220050802.gif<br />
<br />
A 3-button mouse is essential. [http://www.apple.com/mightymouse/ Apple's Mighty Mouse] is an extra treat.<br />
<br />
The Mighty Mouse was superseded in late 2009 by the [http://en.wikipedia.org/wiki/Magic_Mouse Magic Mouse]. Although a great mouse with scrolling capability, the magic mouse is a 2-button mouse with gesture-enabled surface, and so lacks a middle button. To use it choose a 2 button mode in the Mouse menu.<br />
<br />
====PowerMate Dial====<br />
<br />
http://www.griffintechnology.com/assets/images/products/powermate/prod_powermate_sub01b.jpg<br />
<br />
The [http://www.chemistry.ucsc.edu/~wgscott/xtal/powermate_pymol_osx.html PowerMate dial works nicely with pymol].<br />
<br />
====Stereo====<br />
<br />
http://images.apple.com/powermac/images/graphicspymol20051018.jpg<br />
<br />
The [http://www.apple.com/powermac/upgrade.html latest Macs] finally support [http://www.apple.com/powermac/graphics.html stereo in a window]. There is more information in the [[Monitors Hardware Options]] section.<br />
<br />
====Second Monitor====<br />
The trick to getting MacPyMOL to work in stereo on the second monitor is to force it to initially open on that display by providing an appropriate "-X #" (and perhaps -Y #) option on launch. That way the OpenGL context will be created with stereo support.<br />
<source lang="python"><br />
./MacPyMOL.app/Contents/MacOS/MacPyMOL -X -1000<br />
./MacPyMOL.app/Contents/MacOS/MacPyMOL -X -1000 -Y 100<br />
</source><br />
<br />
'''Source:''' ''Warren DeLano; PyMOL Users Archive''<br />
<br />
=Installing X-windows based pymol on Mac OS X=<br />
<br />
===Why would you want to do this?===<br />
<br />
#You want to run a [http://www.oreilly.com/openbook/freedom/ free], guilt-free, open-source version of pymol<br />
#You just happen to prefer the [http://wiki.python.org/moin/TkInter tkinter] menu<br />
#You want to use [http://pymol.sourceforge.net/plugins.html plugins], for example, the [http://www-personal.umich.edu/~mlerner/PyMOL/ apbs plugin] for free grasp-like electrostatic calculations.<br />
<br />
----<br />
<br />
===PyMOL and Fink===<br />
Fink is a subsystem that was created to bring the full power of Linux open-source to the Darwin (Apple) platform. It is essentially a full working Linux system integrated with the Apple OS. Even X11 applications can be run. To use PyMOL with fink, you will first need to install [http://fink.sourceforge.net/ fink]. This usually takes a while, but is straightforward.<br />
<br />
Once fink is installed, you have two options: (1) use the PyMOL package setup by [[User:wgscott|wgscott]], which might be old, but easier to install; or, download the PyMOL source and build. As usual, it comes down to ease of install vs. new features.<br />
<br />
==== PyMOL Directly from Fink ====<br />
To install PyMOL directly from fink, type:<br />
<source lang="bash"><br />
fink install pymol-py25<br />
</source><br />
<br />
This will install python2.5 in fink, along with an X-windows based tkinter. There are also versions that permit you to install PyMOL to interact with python2.4 and even python2.3. Fink uses its own unix-type python installation.<br />
<br />
=====Notes and Possible Issues =====<br />
* The [http://pdb.finkproject.org/pdb/package.php/pymol-py25 fink pymol package] currently exists in the [http://fink.sourceforge.net/faq/usage-fink.php#unstable unstable branch of fink], so you will either have to [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/How_to_Activate_the_Unstable_Branch activate the unstable branch] or make the following symbolic links:<br />
<source lang="bash"><br />
sudo ln -s /sw/fink/dists/unstable/main/finkinfo/sci/pymol-py.* /sw/fink/dists/local/main/finkinfo/.<br />
</source> <br />
You might need to create the latter directory if it doesn't already exist, i.e., issue the command<br />
<source lang="bash"><br />
sudo mkdir -p /sw/fink/dists/local/main/finkinfo<br />
</source><br />
* 10.4 ONLY: Be sure to set your display environment in your start up shell script to use pymol. For example in your home directory, the .bashrc (or .bash_profile) file should contain:<br />
<source lang="bash"><br />
export DISPLAY=":0.0"<br />
</source><br />
Do NOT set the DISPLAY variable for 10.5+, as God does this for you automatically. If for some reason you don't want to set DISPLAY, launch X11 manually (Applications/Utilities) then start a login shell with 'xterm -ls' (note default xterm is not a login shell so will not read .bashrc) and finally issue 'pymol' <br />
* Fink pymol also reads ~/.pymolrc in your home directory.<br />
* I ([[User:wgscott|wgscott]]) have put a whole lot of further information on how to use fink to install crystallographic software on my own [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Main_Page wiki] and [http://chemistry.ucsc.edu/~wgscott/xtal/ website], including instructions on [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Getting_your_fink_installation_to_use_packages_that_I_have_pre-compiled how to install precompiled binary packages using fink].<br />
<br />
* The [http://pdb.finkproject.org/pdb/search.php?summary=pymol fink pymol package] is currently maintained by Jack Howarth.<br />
<br />
<br />
<br />
==== PyMOL Install from Source, Using Fink ====<br />
If the above didn't work, of you really want the latest PyMOL code, then<br />
* Download the latest PyMOL source and unpack it.<br />
* Ensure that you have installed, in Fink:<br />
** python-2.5 pmw-py25<br />
** mesa mesa-shlibs<br />
** libpng3 libpng3-shlibs<br />
** freetype2 freetype2-deve<br />
** freeglut freeglut-shlibs<br />
* Change directory into the new PyMOL dir, eg. ''cd pymol''<br />
* Then, install PyMOL with,<br />
<source lang="bash"><br />
/sw/bin/python setup.py install<br />
</source><br />
<br />
=====Notes and Possible Issues=====<br />
* If you get an error about '''-Wno-long-double''' then your gcc is mismatched. I fixed this by pointing the symbolic link ''/usr/bin/gcc'' from ''/usr/bin/gcc-4.2'' to ''/usr/bin/gcc-4.0''. Or, in code,<br />
<source lang="bash"><br />
# These command are commented out to stop people from copy/pasting b/c <br />
# these are possibly dangerous for your system. Ensure that /usr/bin/gcc<br />
# is a symbolic link and not a real binary. If so, I used the following<br />
# to fix the -Wno-long-double error.<br />
# sudo rm /usr/bin/gcc<br />
# sudo ln -s /usr/bin/gcc-4.0 /usr/bin/gcc<br />
</source><br />
* If you get an error about something like ''GL_PALETTE_TEXTURE'' then you need to comment out those few lines in the code that throws the error. Read the output.<br />
<br />
====Install APBS and friends with fink====<br />
<br />
[[Image:Rna_surface_apbs.png|thumb|APBS calculated electrostatic potential of SARS s2m RNA reveals the colors of a true patriot.]]<br />
<br />
To use the electrostatics plugin, you will need [http://apbs.sourceforge.net/ APBS] and its dependencies. These are also available as fink packages, and include [http://pdb.finkproject.org/pdb/package.php/apbs apbs], [http://pdb.finkproject.org/pdb/package.php/maloc maloc] and [http://pdb.finkproject.org/pdb/package.php/pdb2pqr pdb2pqr]. If you have multiple processors available, you might wish to install the [http://pdb.finkproject.org/pdb/package.php/apbs-mpi-openmpi mpi version of apbs].<br />
<br />
Issuing the command<br />
<br />
fink install apbs<br />
<br />
will install apbs and its required dependencies for you. The fink pymol package is already preconfigured to do the right thing to use apbs as a plugin. Here is [http://xanana.ucsc.edu/xtal/pymol_screenshot.png a big screenshot of the fink APBS package being invoked via the pymol plugin].<br />
<br />
'''Nucleic acids''' may prove problematic for the apbs plugin. If so, use the pdb2pqr command-line tool to create a pqr file manually, instead of using the plugin to generate it.<br />
<br />
----<br />
<br />
===PyMOLX11Hybrid=== <br />
<br />
MacPyMOL for Tiger now includes a hybrid X11 mode. Assuming that X11 is already installed, simply duplicate MacPyMOL.app and rename it "PyMOLX11Hybrid.app" and launch.<br />
<br />
<br />
===PyMOL in MacPorts===<br />
<br />
Recent versions of [http://www.macports.org/ MacPorts] (at least 1.8.2) also include a hybrid PyMOL and also apbs. One can install it with<br />
sudo port install pymol apbs apbs-mpi<br />
<br />
====Pymol with MacPorts via Simple GUI====<br />
<br />
# Install [http://guide.macports.org/#installing MacPorts], including Xcode Tools and X11 if necessary<br />
# Install a MacPorts [http://trac.macports.org/wiki/FAQ#gui GUI client], for example [http://porticus.alittledrop.com/ Porticus]. Do a Selfupdate.<br />
# Search for Pymol via gui and install<br />
# Launch Terminal app and execute pymol<br />
<br />
=====Config issues=====<br />
<br />
* If you already have a .bash_profile, you may need to copy the lines which macports [http://guide.macports.org/#installing.shell installation puts in .profile] into .bash_profile<br />
* Pymol installation in macports uses the subversion repository so you may need to configure the svn command line client [http://svnbook.red-bean.com/en/1.1/ch07.html#svn-ch-7-sect-1.3.1 config file] for your proxy settings in ~/.subversion/servers<br />
* If the menu/control window does not appear when launching pymol and the terminal window reports "ImportError: No module named _tkinter" then force uninstall python26 from macports. Execute the following at the command line to force ignoring on no_tkinter. Python may have installed without tkinter, even though the no_tkinter option was not selected in the gui.<br />
<br />
sudo port install python26 -no_tkinter<br />
<br />
===Troubleshooting===<br />
<br />
; When selecting atoms with the mouse, no matter how well one aims, the atoms selected are actually those far from the ones wanted: This is a known problem. Select "Millions of Colors" in '''System Preferences->Display'''.<br />
; There seems to be a race condition between the Tk window and the openGL window. (The focus for the windows are very quickly flashing back and forth.): This is a well-known problem. The blame here is circular: Apple blames developers, developers blame Apple. Regardless, it appears to have been fixed with the latest Mac OS X (10.6) release. Upgrade to 10.6 and this problem goes away.<br />
;When using multiple displays, the OpenGL window flickers; moving the window between displays crashes the whole session [https://trac.macports.org/ticket/24895]: If you don't need stereo then start PyMOL in mono mode with <pre>pymol -M</pre>If you need stereo then you probably need to wait for a fix in the graphics driver.<br />
<br />
<br />
<br />
<br />
<br />
<br />
[[Category:Nucleic_Acids|MAC Install]]<br />
[[Category:Technical Issues|MAC Install]]</div>Aflaushttps://pymolwiki.org/index.php?title=MAC_Install&diff=8652MAC Install2010-11-14T18:44:18Z<p>Aflaus: /* PyMOL in MacPorts */</p>
<hr />
<div>[[Category:Installation|Mac]]<br />
<br />
__TOC__<br />
<br />
=Installing MacPyMOL=<br />
===Essentials===<br />
The [http://pymol.org/dsc download] is about as straightforward as it gets, and you can install it wherever it makes you happy. You need a 3 button mouse (clickable scroll wheel = middle button). Apple has finally come to its senses and designed a proper, ergonomically pleasant, [http://www.apple.com/mightymouse/ scrollbutton mouse] that works well with pymol and permits horizontal scrolling. Most other mice will also work well.<br />
<br />
===Warning on Mouse Drivers===<br />
<br />
One word of warning: '''Do not install 3rd party drivers''' for multi-button mice if you can avoid it. These often mess with the mapping of the middle button or have other horrific side effects. Fortunately, with OS X, you should not need to.<br />
<br />
===Invoking pymol from the unix command line===<br />
<br />
The unix executable resides at MacPyMOL.app/Contents/MacOS/MacPyMOL<br />
<br />
I ([[User:Wgscott|Bill Scott]]) wrote a cheezy [http://xanana.ucsc.edu/Library/init/zsh/local-functions/xtal/pymol pymol] shell script (and zsh function) to invoke this on the command line. It uses mdfind to find the executable. I also use [[MacOSX-specific .pymolrc file|this ~/.pymolrc]] file.<br />
<br />
Additional invokation options and further details are discussed under [[Launching_PyMOL#MacOS_X:]]<br />
<br />
===Extras===<br />
<br />
You don't need any of these to use MacPyMOL. But you didn't really '''need''' a Mac either. Face it: You need these.<br />
<br />
====Mighty Mouse====<br />
<br />
http://images.apple.com/mightymouse/images/index360scroll220050802.gif<br />
<br />
A 3-button mouse is essential. [http://www.apple.com/mightymouse/ Apple's Mighty Mouse] is an extra treat.<br />
<br />
The Mighty Mouse was superseded in late 2009 by the [http://en.wikipedia.org/wiki/Magic_Mouse Magic Mouse]. Although a great mouse with scrolling capability, the magic mouse is a 2-button mouse with gesture-enabled surface, and so lacks a middle button. To use it choose a 2 button mode in the Mouse menu.<br />
<br />
====PowerMate Dial====<br />
<br />
http://www.griffintechnology.com/assets/images/products/powermate/prod_powermate_sub01b.jpg<br />
<br />
The [http://www.chemistry.ucsc.edu/~wgscott/xtal/powermate_pymol_osx.html PowerMate dial works nicely with pymol].<br />
<br />
====Stereo====<br />
<br />
http://images.apple.com/powermac/images/graphicspymol20051018.jpg<br />
<br />
The [http://www.apple.com/powermac/upgrade.html latest Macs] finally support [http://www.apple.com/powermac/graphics.html stereo in a window]. There is more information in the [[Monitors Hardware Options]] section.<br />
<br />
====Second Monitor====<br />
The trick to getting MacPyMOL to work in stereo on the second monitor is to force it to initially open on that display by providing an appropriate "-X #" (and perhaps -Y #) option on launch. That way the OpenGL context will be created with stereo support.<br />
<source lang="python"><br />
./MacPyMOL.app/Contents/MacOS/MacPyMOL -X -1000<br />
./MacPyMOL.app/Contents/MacOS/MacPyMOL -X -1000 -Y 100<br />
</source><br />
<br />
'''Source:''' ''Warren DeLano; PyMOL Users Archive''<br />
<br />
=Installing X-windows based pymol on Mac OS X=<br />
<br />
===Why would you want to do this?===<br />
<br />
#You want to run a [http://www.oreilly.com/openbook/freedom/ free], guilt-free, open-source version of pymol<br />
#You just happen to prefer the [http://wiki.python.org/moin/TkInter tkinter] menu<br />
#You want to use [http://pymol.sourceforge.net/plugins.html plugins], for example, the [http://www-personal.umich.edu/~mlerner/PyMOL/ apbs plugin] for free grasp-like electrostatic calculations.<br />
<br />
----<br />
<br />
===PyMOL and Fink===<br />
Fink is a subsystem that was created to bring the full power of Linux open-source to the Darwin (Apple) platform. It is essentially a full working Linux system integrated with the Apple OS. Even X11 applications can be run. To use PyMOL with fink, you will first need to install [http://fink.sourceforge.net/ fink]. This usually takes a while, but is straightforward.<br />
<br />
Once fink is installed, you have two options: (1) use the PyMOL package setup by [[User:wgscott|wgscott]], which might be old, but easier to install; or, download the PyMOL source and build. As usual, it comes down to ease of install vs. new features.<br />
<br />
==== PyMOL Directly from Fink ====<br />
To install PyMOL directly from fink, type:<br />
<source lang="bash"><br />
fink install pymol-py25<br />
</source><br />
<br />
This will install python2.5 in fink, along with an X-windows based tkinter. There are also versions that permit you to install PyMOL to interact with python2.4 and even python2.3. Fink uses its own unix-type python installation.<br />
<br />
=====Notes and Possible Issues =====<br />
* The [http://pdb.finkproject.org/pdb/package.php/pymol-py25 fink pymol package] currently exists in the [http://fink.sourceforge.net/faq/usage-fink.php#unstable unstable branch of fink], so you will either have to [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/How_to_Activate_the_Unstable_Branch activate the unstable branch] or make the following symbolic links:<br />
<source lang="bash"><br />
sudo ln -s /sw/fink/dists/unstable/main/finkinfo/sci/pymol-py.* /sw/fink/dists/local/main/finkinfo/.<br />
</source> <br />
You might need to create the latter directory if it doesn't already exist, i.e., issue the command<br />
<source lang="bash"><br />
sudo mkdir -p /sw/fink/dists/local/main/finkinfo<br />
</source><br />
* 10.4 ONLY: Be sure to set your display environment in your start up shell script to use pymol. For example in your home directory, the .bashrc (or .bash_profile) file should contain:<br />
<source lang="bash"><br />
export DISPLAY=":0.0"<br />
</source><br />
Do NOT set the DISPLAY variable for 10.5+, as God does this for you automatically. If for some reason you don't want to set DISPLAY, launch X11 manually (Applications/Utilities) then start a login shell with 'xterm -ls' (note default xterm is not a login shell so will not read .bashrc) and finally issue 'pymol' <br />
* Fink pymol also reads ~/.pymolrc in your home directory.<br />
* I ([[User:wgscott|wgscott]]) have put a whole lot of further information on how to use fink to install crystallographic software on my own [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Main_Page wiki] and [http://chemistry.ucsc.edu/~wgscott/xtal/ website], including instructions on [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Getting_your_fink_installation_to_use_packages_that_I_have_pre-compiled how to install precompiled binary packages using fink].<br />
<br />
* The [http://pdb.finkproject.org/pdb/search.php?summary=pymol fink pymol package] is currently maintained by Jack Howarth.<br />
<br />
<br />
<br />
==== PyMOL Install from Source, Using Fink ====<br />
If the above didn't work, of you really want the latest PyMOL code, then<br />
* Download the latest PyMOL source and unpack it.<br />
* Ensure that you have installed, in Fink:<br />
** python-2.5 pmw-py25<br />
** mesa mesa-shlibs<br />
** libpng3 libpng3-shlibs<br />
** freetype2 freetype2-deve<br />
** freeglut freeglut-shlibs<br />
* Change directory into the new PyMOL dir, eg. ''cd pymol''<br />
* Then, install PyMOL with,<br />
<source lang="bash"><br />
/sw/bin/python setup.py install<br />
</source><br />
<br />
=====Notes and Possible Issues=====<br />
* If you get an error about '''-Wno-long-double''' then your gcc is mismatched. I fixed this by pointing the symbolic link ''/usr/bin/gcc'' from ''/usr/bin/gcc-4.2'' to ''/usr/bin/gcc-4.0''. Or, in code,<br />
<source lang="bash"><br />
# These command are commented out to stop people from copy/pasting b/c <br />
# these are possibly dangerous for your system. Ensure that /usr/bin/gcc<br />
# is a symbolic link and not a real binary. If so, I used the following<br />
# to fix the -Wno-long-double error.<br />
# sudo rm /usr/bin/gcc<br />
# sudo ln -s /usr/bin/gcc-4.0 /usr/bin/gcc<br />
</source><br />
* If you get an error about something like ''GL_PALETTE_TEXTURE'' then you need to comment out those few lines in the code that throws the error. Read the output.<br />
<br />
====Install APBS and friends with fink====<br />
<br />
[[Image:Rna_surface_apbs.png|thumb|APBS calculated electrostatic potential of SARS s2m RNA reveals the colors of a true patriot.]]<br />
<br />
To use the electrostatics plugin, you will need [http://apbs.sourceforge.net/ APBS] and its dependencies. These are also available as fink packages, and include [http://pdb.finkproject.org/pdb/package.php/apbs apbs], [http://pdb.finkproject.org/pdb/package.php/maloc maloc] and [http://pdb.finkproject.org/pdb/package.php/pdb2pqr pdb2pqr]. If you have multiple processors available, you might wish to install the [http://pdb.finkproject.org/pdb/package.php/apbs-mpi-openmpi mpi version of apbs].<br />
<br />
Issuing the command<br />
<br />
fink install apbs<br />
<br />
will install apbs and its required dependencies for you. The fink pymol package is already preconfigured to do the right thing to use apbs as a plugin. Here is [http://xanana.ucsc.edu/xtal/pymol_screenshot.png a big screenshot of the fink APBS package being invoked via the pymol plugin].<br />
<br />
'''Nucleic acids''' may prove problematic for the apbs plugin. If so, use the pdb2pqr command-line tool to create a pqr file manually, instead of using the plugin to generate it.<br />
<br />
----<br />
<br />
===PyMOLX11Hybrid=== <br />
<br />
MacPyMOL for Tiger now includes a hybrid X11 mode. Assuming that X11 is already installed, simply duplicate MacPyMOL.app and rename it "PyMOLX11Hybrid.app" and launch.<br />
<br />
<br />
===PyMOL in MacPorts===<br />
<br />
Recent versions of [http://www.macports.org/ MacPorts] (at least 1.8.2) also include a hybrid PyMOL and also apbs. One can install it with<br />
sudo port install pymol apbs apbs-mpi<br />
<br />
====Pymol with MacPorts via Simple GUI====<br />
<br />
# Install [http://guide.macports.org/#installing MacPorts], including Xcode Tools and X11 if necessary<br />
# Install a MacPorts [http://trac.macports.org/wiki/FAQ#gui GUI client], for example [http://porticus.alittledrop.com/ Porticus]. Do a Selfupdate.<br />
# Search for Pymol via gui and install<br />
# Launch Terminal app and execute pymol<br />
<br />
=====Config issues=====<br />
<br />
* If you already have a .bash_profile, you may need to copy the lines which macports [http://guide.macports.org/#installing.shell installation puts in .profile] into .bash_profile<br />
* Pymol installation in macports uses the subversion repository so you may need to configure the svn command line client [http://svnbook.red-bean.com/en/1.1/ch07.html#svn-ch-7-sect-1.3.1 config file] for your proxy settings in ~/.subversion/servers<br />
<br />
===Troubleshooting===<br />
<br />
; When selecting atoms with the mouse, no matter how well one aims, the atoms selected are actually those far from the ones wanted: This is a known problem. Select "Millions of Colors" in '''System Preferences->Display'''.<br />
; There seems to be a race condition between the Tk window and the openGL window. (The focus for the windows are very quickly flashing back and forth.): This is a well-known problem. The blame here is circular: Apple blames developers, developers blame Apple. Regardless, it appears to have been fixed with the latest Mac OS X (10.6) release. Upgrade to 10.6 and this problem goes away.<br />
;When using multiple displays, the OpenGL window flickers; moving the window between displays crashes the whole session [https://trac.macports.org/ticket/24895]: If you don't need stereo then start PyMOL in mono mode with <pre>pymol -M</pre>If you need stereo then you probably need to wait for a fix in the graphics driver.<br />
<br />
<br />
<br />
<br />
<br />
<br />
[[Category:Nucleic_Acids|MAC Install]]<br />
[[Category:Technical Issues|MAC Install]]</div>Aflaushttps://pymolwiki.org/index.php?title=MAC_Install&diff=8651MAC Install2010-11-14T18:10:31Z<p>Aflaus: /* Mighty Mouse */</p>
<hr />
<div>[[Category:Installation|Mac]]<br />
<br />
__TOC__<br />
<br />
=Installing MacPyMOL=<br />
===Essentials===<br />
The [http://pymol.org/dsc download] is about as straightforward as it gets, and you can install it wherever it makes you happy. You need a 3 button mouse (clickable scroll wheel = middle button). Apple has finally come to its senses and designed a proper, ergonomically pleasant, [http://www.apple.com/mightymouse/ scrollbutton mouse] that works well with pymol and permits horizontal scrolling. Most other mice will also work well.<br />
<br />
===Warning on Mouse Drivers===<br />
<br />
One word of warning: '''Do not install 3rd party drivers''' for multi-button mice if you can avoid it. These often mess with the mapping of the middle button or have other horrific side effects. Fortunately, with OS X, you should not need to.<br />
<br />
===Invoking pymol from the unix command line===<br />
<br />
The unix executable resides at MacPyMOL.app/Contents/MacOS/MacPyMOL<br />
<br />
I ([[User:Wgscott|Bill Scott]]) wrote a cheezy [http://xanana.ucsc.edu/Library/init/zsh/local-functions/xtal/pymol pymol] shell script (and zsh function) to invoke this on the command line. It uses mdfind to find the executable. I also use [[MacOSX-specific .pymolrc file|this ~/.pymolrc]] file.<br />
<br />
Additional invokation options and further details are discussed under [[Launching_PyMOL#MacOS_X:]]<br />
<br />
===Extras===<br />
<br />
You don't need any of these to use MacPyMOL. But you didn't really '''need''' a Mac either. Face it: You need these.<br />
<br />
====Mighty Mouse====<br />
<br />
http://images.apple.com/mightymouse/images/index360scroll220050802.gif<br />
<br />
A 3-button mouse is essential. [http://www.apple.com/mightymouse/ Apple's Mighty Mouse] is an extra treat.<br />
<br />
The Mighty Mouse was superseded in late 2009 by the [http://en.wikipedia.org/wiki/Magic_Mouse Magic Mouse]. Although a great mouse with scrolling capability, the magic mouse is a 2-button mouse with gesture-enabled surface, and so lacks a middle button. To use it choose a 2 button mode in the Mouse menu.<br />
<br />
====PowerMate Dial====<br />
<br />
http://www.griffintechnology.com/assets/images/products/powermate/prod_powermate_sub01b.jpg<br />
<br />
The [http://www.chemistry.ucsc.edu/~wgscott/xtal/powermate_pymol_osx.html PowerMate dial works nicely with pymol].<br />
<br />
====Stereo====<br />
<br />
http://images.apple.com/powermac/images/graphicspymol20051018.jpg<br />
<br />
The [http://www.apple.com/powermac/upgrade.html latest Macs] finally support [http://www.apple.com/powermac/graphics.html stereo in a window]. There is more information in the [[Monitors Hardware Options]] section.<br />
<br />
====Second Monitor====<br />
The trick to getting MacPyMOL to work in stereo on the second monitor is to force it to initially open on that display by providing an appropriate "-X #" (and perhaps -Y #) option on launch. That way the OpenGL context will be created with stereo support.<br />
<source lang="python"><br />
./MacPyMOL.app/Contents/MacOS/MacPyMOL -X -1000<br />
./MacPyMOL.app/Contents/MacOS/MacPyMOL -X -1000 -Y 100<br />
</source><br />
<br />
'''Source:''' ''Warren DeLano; PyMOL Users Archive''<br />
<br />
=Installing X-windows based pymol on Mac OS X=<br />
<br />
===Why would you want to do this?===<br />
<br />
#You want to run a [http://www.oreilly.com/openbook/freedom/ free], guilt-free, open-source version of pymol<br />
#You just happen to prefer the [http://wiki.python.org/moin/TkInter tkinter] menu<br />
#You want to use [http://pymol.sourceforge.net/plugins.html plugins], for example, the [http://www-personal.umich.edu/~mlerner/PyMOL/ apbs plugin] for free grasp-like electrostatic calculations.<br />
<br />
----<br />
<br />
===PyMOL and Fink===<br />
Fink is a subsystem that was created to bring the full power of Linux open-source to the Darwin (Apple) platform. It is essentially a full working Linux system integrated with the Apple OS. Even X11 applications can be run. To use PyMOL with fink, you will first need to install [http://fink.sourceforge.net/ fink]. This usually takes a while, but is straightforward.<br />
<br />
Once fink is installed, you have two options: (1) use the PyMOL package setup by [[User:wgscott|wgscott]], which might be old, but easier to install; or, download the PyMOL source and build. As usual, it comes down to ease of install vs. new features.<br />
<br />
==== PyMOL Directly from Fink ====<br />
To install PyMOL directly from fink, type:<br />
<source lang="bash"><br />
fink install pymol-py25<br />
</source><br />
<br />
This will install python2.5 in fink, along with an X-windows based tkinter. There are also versions that permit you to install PyMOL to interact with python2.4 and even python2.3. Fink uses its own unix-type python installation.<br />
<br />
=====Notes and Possible Issues =====<br />
* The [http://pdb.finkproject.org/pdb/package.php/pymol-py25 fink pymol package] currently exists in the [http://fink.sourceforge.net/faq/usage-fink.php#unstable unstable branch of fink], so you will either have to [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/How_to_Activate_the_Unstable_Branch activate the unstable branch] or make the following symbolic links:<br />
<source lang="bash"><br />
sudo ln -s /sw/fink/dists/unstable/main/finkinfo/sci/pymol-py.* /sw/fink/dists/local/main/finkinfo/.<br />
</source> <br />
You might need to create the latter directory if it doesn't already exist, i.e., issue the command<br />
<source lang="bash"><br />
sudo mkdir -p /sw/fink/dists/local/main/finkinfo<br />
</source><br />
* 10.4 ONLY: Be sure to set your display environment in your start up shell script to use pymol. For example in your home directory, the .bashrc (or .bash_profile) file should contain:<br />
<source lang="bash"><br />
export DISPLAY=":0.0"<br />
</source><br />
Do NOT set the DISPLAY variable for 10.5+, as God does this for you automatically. If for some reason you don't want to set DISPLAY, launch X11 manually (Applications/Utilities) then start a login shell with 'xterm -ls' (note default xterm is not a login shell so will not read .bashrc) and finally issue 'pymol' <br />
* Fink pymol also reads ~/.pymolrc in your home directory.<br />
* I ([[User:wgscott|wgscott]]) have put a whole lot of further information on how to use fink to install crystallographic software on my own [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Main_Page wiki] and [http://chemistry.ucsc.edu/~wgscott/xtal/ website], including instructions on [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Getting_your_fink_installation_to_use_packages_that_I_have_pre-compiled how to install precompiled binary packages using fink].<br />
<br />
* The [http://pdb.finkproject.org/pdb/search.php?summary=pymol fink pymol package] is currently maintained by Jack Howarth.<br />
<br />
<br />
<br />
==== PyMOL Install from Source, Using Fink ====<br />
If the above didn't work, of you really want the latest PyMOL code, then<br />
* Download the latest PyMOL source and unpack it.<br />
* Ensure that you have installed, in Fink:<br />
** python-2.5 pmw-py25<br />
** mesa mesa-shlibs<br />
** libpng3 libpng3-shlibs<br />
** freetype2 freetype2-deve<br />
** freeglut freeglut-shlibs<br />
* Change directory into the new PyMOL dir, eg. ''cd pymol''<br />
* Then, install PyMOL with,<br />
<source lang="bash"><br />
/sw/bin/python setup.py install<br />
</source><br />
<br />
=====Notes and Possible Issues=====<br />
* If you get an error about '''-Wno-long-double''' then your gcc is mismatched. I fixed this by pointing the symbolic link ''/usr/bin/gcc'' from ''/usr/bin/gcc-4.2'' to ''/usr/bin/gcc-4.0''. Or, in code,<br />
<source lang="bash"><br />
# These command are commented out to stop people from copy/pasting b/c <br />
# these are possibly dangerous for your system. Ensure that /usr/bin/gcc<br />
# is a symbolic link and not a real binary. If so, I used the following<br />
# to fix the -Wno-long-double error.<br />
# sudo rm /usr/bin/gcc<br />
# sudo ln -s /usr/bin/gcc-4.0 /usr/bin/gcc<br />
</source><br />
* If you get an error about something like ''GL_PALETTE_TEXTURE'' then you need to comment out those few lines in the code that throws the error. Read the output.<br />
<br />
====Install APBS and friends with fink====<br />
<br />
[[Image:Rna_surface_apbs.png|thumb|APBS calculated electrostatic potential of SARS s2m RNA reveals the colors of a true patriot.]]<br />
<br />
To use the electrostatics plugin, you will need [http://apbs.sourceforge.net/ APBS] and its dependencies. These are also available as fink packages, and include [http://pdb.finkproject.org/pdb/package.php/apbs apbs], [http://pdb.finkproject.org/pdb/package.php/maloc maloc] and [http://pdb.finkproject.org/pdb/package.php/pdb2pqr pdb2pqr]. If you have multiple processors available, you might wish to install the [http://pdb.finkproject.org/pdb/package.php/apbs-mpi-openmpi mpi version of apbs].<br />
<br />
Issuing the command<br />
<br />
fink install apbs<br />
<br />
will install apbs and its required dependencies for you. The fink pymol package is already preconfigured to do the right thing to use apbs as a plugin. Here is [http://xanana.ucsc.edu/xtal/pymol_screenshot.png a big screenshot of the fink APBS package being invoked via the pymol plugin].<br />
<br />
'''Nucleic acids''' may prove problematic for the apbs plugin. If so, use the pdb2pqr command-line tool to create a pqr file manually, instead of using the plugin to generate it.<br />
<br />
----<br />
<br />
===PyMOLX11Hybrid=== <br />
<br />
MacPyMOL for Tiger now includes a hybrid X11 mode. Assuming that X11 is already installed, simply duplicate MacPyMOL.app and rename it "PyMOLX11Hybrid.app" and launch.<br />
<br />
<br />
===PyMOL in MacPorts===<br />
<br />
Recent versions of [http://www.macports.org/ MacPorts] (at least 1.8.2) also include a hybrid PyMOL and also apbs. One can install it with<br />
sudo port install pymol apbs apbs-mpi<br />
<br />
<br />
===Troubleshooting===<br />
<br />
; When selecting atoms with the mouse, no matter how well one aims, the atoms selected are actually those far from the ones wanted: This is a known problem. Select "Millions of Colors" in '''System Preferences->Display'''.<br />
; There seems to be a race condition between the Tk window and the openGL window. (The focus for the windows are very quickly flashing back and forth.): This is a well-known problem. The blame here is circular: Apple blames developers, developers blame Apple. Regardless, it appears to have been fixed with the latest Mac OS X (10.6) release. Upgrade to 10.6 and this problem goes away.<br />
;When using multiple displays, the OpenGL window flickers; moving the window between displays crashes the whole session [https://trac.macports.org/ticket/24895]: If you don't need stereo then start PyMOL in mono mode with <pre>pymol -M</pre>If you need stereo then you probably need to wait for a fix in the graphics driver.<br />
<br />
<br />
<br />
<br />
<br />
<br />
[[Category:Nucleic_Acids|MAC Install]]<br />
[[Category:Technical Issues|MAC Install]]</div>Aflaushttps://pymolwiki.org/index.php?title=Examples_of_nucleic_acid_cartoons&diff=4524Examples of nucleic acid cartoons2007-12-09T19:20:10Z<p>Aflaus: </p>
<hr />
<div>== Default settings ==<br />
The defaults give a phosphate backbone with single sticks passing across the full width of the base plane.<br />
<source lang="python"><br />
set cartoon_nucleic_acid_mode, 1 # backbone follows phosphates<br />
set cartoon_ladder_mode, 1 # sticks from backbone into nucleotide<br />
set cartoon_ring_mode, 0 # no nucleotide rings<br />
set cartoon_ring_finder, 1 # ribose and base rings (not displayed since ring mode 0)<br />
</source><br />
{|<br />
|[[Image:DNA-default-ring0-ladder1-na0-finder1.png|default view|thumb]]<br />
|}<br />
== Cartoon ring mode ==<br />
<br />
=== Settings ===<br />
<br />
<pre>set cartoon_ring_mode, value</pre><br />
{|}<br />
!value !!align="left"| effect<br />
|-<br />
|align="center" | 0 || stick from backbone atom to N1 of purines and N3 of pyrimidines<br />
|-<br />
|align="center" | 1 || simple plane for ribose and base rings covering area between ring bonds<br />
|-<br />
|align="center" | 2 || simple plane for ribose and base rings covering area inside sticks (slightly smaller than mode 1)<br />
|-<br />
|align="center" | 3 || plane bounded by sticks for ribose and base rings<br />
|-<br />
|align="center" | 4 || large sphere of ring diameter at centre of ribose and each base ring<br />
|-<br />
|align="center" | 5 || small sphere of 1/10 diameter at centre of ribose and each base ring<br />
|}<br />
<br />
=== Examples ===<br />
<br />
{|<br />
|[[Image:DNA-ring0-ladder1-na0-finder1.png|cartoon_ring_mode,0|thumb]]<br />
|[[Image:DNA-ring1-ladder1-na0-finder1.png|cartoon_ring_mode,1|thumb]]<br />
|[[Image:DNA-ring2-ladder1-na0-finder1.png|cartoon_ring_mode,2|thumb]]<br />
|[[Image:DNA-ring3-ladder1-na0-finder1.png|cartoon_ring_mode,3|thumb]]<br />
|[[Image:DNA-ring4-ladder1-na0-finder1.png|cartoon_ring_mode,4|thumb]]<br />
|[[Image:DNA-ring5-ladder1-na0-finder1.png|cartoon_ring_mode,5|thumb]]<br />
|}<br />
<center>all with defaults:&nbsp;<i>cartoon_ladder_mode,1&nbsp;&nbsp;&nbsp;cartoon_nucleic_acid_mode,0&nbsp;&nbsp;&nbsp;cartoon_ring_finder,1</i></center><br />
<br />
== Cartoon ring finder ==<br />
<br />
=== Settings ===<br />
<pre>set cartoon_ring_finder, value</pre><br />
{|<br />
!value !! align="left" | effect<br />
|-<br />
|align="center" | 0 || no rings or sticks joining them<br />
|-<br />
|align="center" | 1 || both ribose and base ring<br />
|-<br />
|align="center" | 2 || only base ring(s), stick connects directly from phosphate to ring<br />
|-<br />
|align="center" | 3 || very similar to ring finder 1, slight effect on transparency = distinct behaviour?<br />
|-<br />
|align="center" | 4 || very similar to ring finder 1, slight effect on transparency = distinct behaviour?<br />
|-<br />
|align="center" | 5 || sticks visible but rings invisible<br />
|}<br />
<br />
=== Examples ===<br />
<br />
{|<br />
|[[Image:DNA-ring3-ladder1-na0-finder0.png|cartoon_ring_finder,0|thumb]]<br />
|[[Image:DNA-ring3-ladder1-na0-finder1.png|cartoon_ring_finder,1|thumb]]<br />
|[[Image:DNA-ring3-ladder1-na0-finder2.png|cartoon_ring_finder,2|thumb]]<br />
|[[Image:DNA-ring3-ladder1-na0-finder3.png|cartoon_ring_finder,3|thumb]]<br />
|[[Image:DNA-ring3-ladder1-na0-finder4.png|cartoon_ring_finder,4|thumb]]<br />
|[[Image:DNA-ring3-ladder1-na0-finder5.png|cartoon_ring_finder,5|thumb]]<br />
|}<br />
all with:&nbsp;<i>cartoon_ladder_mode,1&nbsp;&nbsp;&nbsp;cartoon_ring_mode,3&nbsp;&nbsp;&nbsp;cartoon_nucleic_acid_mode,0</i><br />
<br />
== Cartoon ladder mode ==<br />
<br />
=== Settings ===<br />
<br />
<pre>set cartoon_ladder_mode, value</pre><br />
{|<br />
!value !! align="left" | effect<br />
|-<br />
|align="center" | 0 || no sticks shown<br />
|-<br />
|align="center" | 1 || sticks show<br />
|}<br />
<br />
=== Examples ===<br />
<br />
{|<br />
|[[Image:DNA-ring3-ladder0-na0-finder1.png|cartoon_ladder_mode,0|thumb]]<br />
|[[Image:DNA-ring3-ladder1-na0-finder1.png|cartoon_ladder_mode,1|thumb]]<br />
|}<br />
all with:&nbsp;<i>cartoon_ring_mode,3&nbsp;&nbsp;&nbsp;cartoon_nucleic_acid_mode,0&nbsp;&nbsp;&nbsp;cartoon_ring_finder,1</i><br />
<br />
Note that the visibility of the ladder sticks depends on ring mode >0, ring finder >0, nucleic acid mode = 0<br />
<br />
== Cartoon nucleic acid mode ==<br />
<br />
=== Settings ===<br />
<br />
<pre>set cartoon_nucleic_acid_mode, value</pre><br />
{|<br />
!value !! align="left" | effect<br />
|-<br />
|align="center" |0 || smooth backbone passing through phosphorus atoms, backbone terminates at last phosphorus on either end of chain <br />
|-<br />
|align="center" | 1 || smooth backbone passing through ribose C3' atoms, backbone terminates at last C3' on either end of chain<br />
|-<br />
|align="center" | 2 || smooth backbone passing through phosphorus atoms, backbone terminates at last phosphorus on 5' end and O3' on 3' end (note takes O3' colour at terminus in default colouring)<br />
|-<br />
|align="center" | 3 || appears same as mode 0?<br />
|-<br />
|align="center" | 4 || appears same as mode 2?<br />
|}<br />
<br />
=== Examples ===<br />
<br />
{|<br />
|[[Image:DNA-ring3-ladder1-na0-finder1.png|cartoon_nucleic_acid_mode,0|thumb]]<br />
|[[Image:DNA-ring3-ladder1-na1-finder1.png|cartoon_nucleic_acid_mode,1|thumb]]<br />
|[[Image:DNA-ring3-ladder1-na2-finder1.png|cartoon_nucleic_acid_mode,2|thumb]]<br />
|[[Image:DNA-ring3-ladder1-na3-finder1.png|cartoon_nucleic_acid_mode,3|thumb]]<br />
|[[Image:DNA-ring3-ladder1-na4-finder1.png|cartoon_nucleic_acid_mode,4|thumb]]<br />
|}<br />
all with:&nbsp;<i>cartoon_ladder_mode,0&nbsp;&nbsp;&nbsp;cartoon_ring_mode,3&nbsp;&nbsp;&nbsp;cartoon_ring_finder,1</i><br />
<br />
[[Category:Nucleic_Acids|Cartoon ring and cartoon ladder settings]]</div>Aflaushttps://pymolwiki.org/index.php?title=File:DNA-ring3-ladder1-na4-finder1.png&diff=4523File:DNA-ring3-ladder1-na4-finder1.png2007-12-09T19:18:00Z<p>Aflaus: </p>
<hr />
<div></div>Aflaushttps://pymolwiki.org/index.php?title=File:DNA-ring3-ladder1-na3-finder1.png&diff=4522File:DNA-ring3-ladder1-na3-finder1.png2007-12-09T19:17:35Z<p>Aflaus: </p>
<hr />
<div></div>Aflaushttps://pymolwiki.org/index.php?title=File:DNA-ring3-ladder1-na2-finder1.png&diff=4521File:DNA-ring3-ladder1-na2-finder1.png2007-12-09T19:17:07Z<p>Aflaus: </p>
<hr />
<div></div>Aflaushttps://pymolwiki.org/index.php?title=File:DNA-ring3-ladder1-na1-finder1.png&diff=4520File:DNA-ring3-ladder1-na1-finder1.png2007-12-09T19:16:45Z<p>Aflaus: </p>
<hr />
<div></div>Aflaushttps://pymolwiki.org/index.php?title=File:DNA-ring3-ladder0-na0-finder1.png&diff=4519File:DNA-ring3-ladder0-na0-finder1.png2007-12-09T19:15:52Z<p>Aflaus: </p>
<hr />
<div></div>Aflaushttps://pymolwiki.org/index.php?title=File:DNA-ring3-ladder1-na0-finder5.png&diff=4518File:DNA-ring3-ladder1-na0-finder5.png2007-12-09T19:14:54Z<p>Aflaus: </p>
<hr />
<div></div>Aflaushttps://pymolwiki.org/index.php?title=File:DNA-ring3-ladder1-na0-finder4.png&diff=4517File:DNA-ring3-ladder1-na0-finder4.png2007-12-09T19:14:33Z<p>Aflaus: </p>
<hr />
<div></div>Aflaushttps://pymolwiki.org/index.php?title=File:DNA-ring3-ladder1-na0-finder3.png&diff=4516File:DNA-ring3-ladder1-na0-finder3.png2007-12-09T19:14:09Z<p>Aflaus: </p>
<hr />
<div></div>Aflaushttps://pymolwiki.org/index.php?title=File:DNA-ring3-ladder1-na0-finder2.png&diff=4515File:DNA-ring3-ladder1-na0-finder2.png2007-12-09T19:13:39Z<p>Aflaus: </p>
<hr />
<div></div>Aflaushttps://pymolwiki.org/index.php?title=File:DNA-ring3-ladder1-na0-finder0.png&diff=4514File:DNA-ring3-ladder1-na0-finder0.png2007-12-09T19:13:13Z<p>Aflaus: </p>
<hr />
<div></div>Aflaushttps://pymolwiki.org/index.php?title=File:DNA-ring5-ladder1-na0-finder1.png&diff=4513File:DNA-ring5-ladder1-na0-finder1.png2007-12-09T19:11:56Z<p>Aflaus: </p>
<hr />
<div></div>Aflaushttps://pymolwiki.org/index.php?title=File:DNA-ring4-ladder1-na0-finder1.png&diff=4512File:DNA-ring4-ladder1-na0-finder1.png2007-12-09T19:11:34Z<p>Aflaus: </p>
<hr />
<div></div>Aflaushttps://pymolwiki.org/index.php?title=File:DNA-ring3-ladder1-na0-finder1.png&diff=4511File:DNA-ring3-ladder1-na0-finder1.png2007-12-09T19:09:32Z<p>Aflaus: </p>
<hr />
<div></div>Aflaushttps://pymolwiki.org/index.php?title=File:DNA-ring2-ladder1-na0-finder1.png&diff=4510File:DNA-ring2-ladder1-na0-finder1.png2007-12-09T19:09:00Z<p>Aflaus: </p>
<hr />
<div></div>Aflaushttps://pymolwiki.org/index.php?title=File:DNA-ring1-ladder1-na0-finder1.png&diff=4509File:DNA-ring1-ladder1-na0-finder1.png2007-12-09T19:08:18Z<p>Aflaus: </p>
<hr />
<div></div>Aflaushttps://pymolwiki.org/index.php?title=File:DNA-ring0-ladder1-na0-finder1.png&diff=4508File:DNA-ring0-ladder1-na0-finder1.png2007-12-09T19:07:40Z<p>Aflaus: </p>
<hr />
<div></div>Aflaushttps://pymolwiki.org/index.php?title=File:DNA-default-ring0-ladder1-na0-finder1.png&diff=4507File:DNA-default-ring0-ladder1-na0-finder1.png2007-12-09T19:04:51Z<p>Aflaus: </p>
<hr />
<div></div>Aflaushttps://pymolwiki.org/index.php?title=Cartoon&diff=4506Cartoon2007-12-09T18:29:17Z<p>Aflaus: /* Other Nucleic Acids & Cartoon Settings */</p>
<hr />
<div>==Cartoon Command==<br />
===DESCRIPTION===<br />
'''cartoon''' changes the default cartoon for a set of atoms.<br />
<br />
===USAGE===<br />
cartoon type, (selection)<br />
<br />
type = skip | automatic | loop | rectangle | oval | tube | arrow | dumbbell<br />
<br />
===PYMOL API===<br />
<source lang="python"><br />
cmd.cartoon(string type, string selection )<br />
</source><br />
<br />
===EXAMPLES===<br />
cartoon rectangle,(chain A)<br />
cartoon skip,(resi 145:156)<br />
<br />
===NOTES===<br />
the "automatic" mode utilizes ribbons according to the information in the PDB HELIX and SHEET records.<br />
<br />
==Adjusting width of cartoon==<br />
Try varying the following.<br />
<br />
For &beta;-strands:<br />
<source lang="python"><br />
cartoon_rect_length<br />
cartoon_rect_width<br />
</source><br />
<br />
For &alpha;-helices:<br />
<source lang="python"><br />
cartoon_oval_length<br />
cartoon_oval_width<br />
</source><br />
<br />
For loops:<br />
<source lang="python"><br />
cartoon_loop_radius<br />
</source><br />
<br />
For "fancy" &alpha;-helices:<br />
<source lang="python"><br />
cartoon_dumbell_length<br />
cartoon_dumbell_width<br />
cartoon_dumbell_radius (radius of cylinder at edge of helix ribbon)<br />
</source><br />
<br />
In each case "length" refers to what some might call the width and "width" refers to what some might call the thickness.<br />
<br />
<br />
[[Image:Cartoon_ex.png|thumb|center|Cartoon Representation Example|300px]]<br />
<br />
<br />
===Forcing Exact Boundaries in Coloring Secondary Structures===<br />
To force PyMol to respect secondary structural elements color-wise (PyMol smooths out colors near color chagnes for a prettier image) use the following <br />
PyMol command:<br />
<code><br />
set cartoon_discrete_colors, on<br />
</code><br />
<br />
[[Image:Cartoon_discrete_color0.png|Discrete Coloring Off|center|thumb]] [[Image:Cartoon_discrete_color1.png|Discrete Coloring On|center|thumb]]<br />
<br />
== Sausage Representation ==<br />
The familiar sausage representation in PyMol is called, "putty". To enable the putty/sausage view simply do,<br />
show cartoon<br />
cartoon putty<br />
unset cartoon_smooth_loops<br />
unset cartoon_flat_sheets<br />
<br />
As of v 0.98 or so, there's a Putty option. Use this.<br />
<br />
[[Image:B_factor_putty.png|thumb|Example of B-factor Putty|center|250px]]<br />
<br />
==Black and White Representation==<br />
'''UPDATE''': This method is essentially obseleted by the new setting '''set ray_trace_mode,2'''. More information on this at [[Ray]].<br />
For those who want a nifty black and white representation of their protein try the following:<br />
# Ray trace your protein of choice in a cartoon representation use a BLACK background<br />
# Save the image<br />
# Load the image in GIMP. [[Image:Bw1.jpeg|thumb|Black BG Ribbon|center|350px]]<br />
# Desaturate or Grayscale the image. [[Image:Bw2.jpeg|thumb|Grayscale|center|350px]]<br />
# Run the filter: Filter->Edge-Detect->Edge. [[Image:Bw3.jpeg|thumb|Edge Detect|center|350px]]<br />
# Select: Layers->Color->Invert. [[Image:Bw4.jpeg|thumb|Invert Color|center|350px]]<br />
# Different methods of edge detection will give you different results. In the last example, I used Laplace Edge-Detect, then painted an all white layer beneath the current layer to achieve the results. [[Image:Bw5.jpeg|thumb|Other Styles|center|350px|Comments]]<br />
<br />
<br />
I'm sure there are other ways to do this. If you want to include it in a publication make sure you ray traced it large enough. For that, see [[:Category:Advanced_Issues_Image_Manipulation_Publication_Quatlity_Images|Creating Publication Quality Images]].<br />
<br />
==CA (Alpha Carbon) Trace==<br />
If you have a structure with just a alpha carbon trace, you can get a cartoon by<br />
<source lang="python"><br />
set cartoon_trace,1<br />
show cartoon<br />
</source><br />
If your structure is more than just the CA backbone, the cartoon representation will look incorrect, so use it just with CA trace.<br />
<br />
==Various Transparency Levels==<br />
[[Image:Cartoon_multi_transp.png|thumb|center|Example of Cartoon Multi-level Transparency. The near cartoon has transparency setting '''0.2''', the segment in the BG '''0.5'''.]]<br />
One can make different cartoon selections have different transparency values, in PyMol. The trick here is to use "create" instead of "select". Create makes new objects that can have independent settings. <br />
<br />
<source lang="python"><br />
load mol_obj.pdb<br />
<br />
# transfer a piece of the molecule into a new object<br />
<br />
create new_obj, chain A<br />
remove mol_obj in new_obj<br />
<br />
# adjust trasparency for the new object<br />
<br />
set cartoon_transparency, 0.5, new_obj<br />
</source><br />
<br />
== Nucleic Acid Representation ==<br />
[[Image:Nucleic1.png|thumb|center|Showing Nucleic Acids]]<br />
To show nucleic acids in a nicer format do:<br />
<source lang="python"><br />
set cartoon_ring_mode,1<br />
show cartoon<br />
</source><br />
<br />
=== Other Nucleic Acids & Cartoon Settings ===<br />
Here are some things to try:<br />
<source lang="python"><br />
set cartoon_ring_mode, 1 # (or 2 or 3)<br />
set cartoon_ring_finder, 1 # (or 2 or 3 or 4)<br />
set cartoon_nucleic_acid_mode, 0 # (or 1 or 2 or 3 or 4)<br />
<br />
set cartoon_side_chain_helper<br />
rebuild<br />
<br />
set cartoon_ring_transparency, 0.5<br />
<br />
set cartoon_ladder_mode, 0 # or 1<br />
<br />
set cartoon_ladder_color, color-name<br />
set cartoon_nucleic_acid_color, color-name<br />
<br />
cartoon oval<br />
set cartoon_oval_width, 0.8<br />
<br />
cartoon rect<br />
<br />
cartoon dumbbell<br />
set cartoon_dumbbell_width, 0.4<br />
set cartoon_dumbbell_radius, 0.4<br />
</source><br />
[[Overview of nucleic acid cartoons]]<br />
<br />
[[Examples of nucleic acid cartoons]]<br />
<br />
== See Also ==<br />
[[Displaying_Biochemical_Properties]]<br />
<br />
[[Category:Representations|Cartoon]]<br />
[[Category:Nucleic_Acids|Cartoon]]</div>Aflaushttps://pymolwiki.org/index.php?title=Nucleic_acid_cartoon_settings&diff=4505Nucleic acid cartoon settings2007-12-09T18:28:44Z<p>Aflaus: Nucleic acid cartoon settings moved to Overview of nucleic acid cartoons</p>
<hr />
<div>#REDIRECT [[Overview of nucleic acid cartoons]]</div>Aflaushttps://pymolwiki.org/index.php?title=Overview_of_nucleic_acid_cartoons&diff=4504Overview of nucleic acid cartoons2007-12-09T18:28:44Z<p>Aflaus: Nucleic acid cartoon settings moved to Overview of nucleic acid cartoons</p>
<hr />
<div>== Overview ==<br />
<br />
Pymol has a complex group of settings for controlling the way nucleic acids are represented, broadly separated into:<br />
* ring, for ribose and base ring(s)<br />
* ladder, for the sticks connecting the backbone, ribose and base ring(s)<br />
* nucleic acid, for the smooth backbone path<br />
<br />
Each setting can be altered with the set command. The cartoon settings affect each other so experimentation may be necessary to achieve what you want. Many of the mode settings only seem to work at the global level and cannot be applied to individual objects or selections.<br />
<br />
== Ring settings ==<br />
<br />
=== Ring mode ===<br />
<br />
Ring mode defines the representation of the ribose and base.<br />
<pre>set cartoon_ring_mode, value</pre><br />
{|<br />
!value !!align="left"| effect<br />
|-<br />
|align="center" | 0 || stick from backbone atom to N1 of purines and N3 of pyrimidines<br />
|-<br />
|align="center" | 1 || simple plane for ribose and base rings covering area between ring bonds<br />
|-<br />
|align="center" | 2 || simple plane for ribose and base rings covering area inside sticks (slightly smaller than mode 1)<br />
|-<br />
|align="center" | 3 || plane bounded by sticks for ribose and base rings<br />
|-<br />
|align="center" | 4 || large sphere of ring diameter at centre of ribose and each base ring<br />
|-<br />
|align="center" | 5 || small sphere of 1/10 diameter at centre of ribose and each base ring<br />
|-<br />
|align="center" | 6+ || appears to default to ring mode 2<br />
|}<br />
=== Ring finder ===<br />
<br />
Ring finder defines the rings which are recognised<br />
<pre>set cartoon_ring_finder, value</pre><br />
{|<br />
!value !! align="left" | effect<br />
|-<br />
|align="center" | 0 || no rings or sticks joining them<br />
|-<br />
|align="center" | 1 || both ribose and base ring<br />
|-<br />
|align="center" | 2 || only base ring(s), stick connects directly from phosphate to ring<br />
|-<br />
|align="center" | 3 || very similar to ring finder 1, slight effect on transparency = distinct behaviour?<br />
|-<br />
|align="center" | 4 || very similar to ring finder 1, slight effect on transparency = distinct behaviour?<br />
|-<br />
|align="center" | 5 || sticks visible but rings invisible<br />
|-<br />
|align="center" | 6+ || appears to default to ring finder 5<br />
|}<br />
<br />
=== Other settings for ring ===<br />
<pre>set cartoon_ring_xxx, value</pre><br />
{|<br />
! align="center" | xxx !! value !! align="left" | effect<br />
|-<br />
|align="center" | color || align="center" |color || set the colour of the ring or sphere<br />
|-<br />
|align="center" | width || align="center" | float || thickness of ring for planes and sticks (modes 1, 2, 3)<br />
|-<br />
|align="center" | radius || align="center" |float || radius of ring for spheres (modes 4, 5), negative number gives sphere of same radius as ring in mode 4, approx 1/10 ring diameter in mode 5<br />
|-<br />
|align="center" | transparency || align="center" |float || transparency of ring or sphere, does not affect sticks in ring mode 3<br />
|}<br />
<br />
== Ladder settings ==<br />
<br />
=== Ladder mode ===<br />
<br />
Ladder mode affects the sticks connecting the backbone to ribose and ribose to base, and ring mode 0 or ring finder 5.<br />
<pre>set cartoon_ladder_mode, value</pre><br />
{|<br />
!value !! align="left" | effect<br />
|-<br />
|align="center" | 0 || no sticks shown<br />
|-<br />
|align="center" | 1 || sticks show<br />
|-<br />
|align="center" | 2+ || appears to default to ladder mode 1<br />
|}<br />
=== Other settings for ladder ===<br />
<pre>set cartoon_ladder_xxx, value</pre><br />
{|<br />
! align="center" | xxx !! value !! align="left" | effect<br />
|-<br />
|align="center" | color || color || colour of the stick<br />
|-<br />
|align="center" | radius || float || stick width for ring modes 1, 4 and 5 (default is 0.25), in other ring modes the ladder stick width is controlled by the ring width instead<br />
|}<br />
<br />
== Nucleic acid settings ==<br />
<br />
=== Nucleic acid mode ===<br />
<pre>set cartoon_nucleic_acid_mode, value</pre><br />
{|<br />
!value !! align="left" | effect<br />
|-<br />
|align="center" |0 || smooth backbone passing through phosphorus atoms, backbone terminates at last phosphorus on either end of chain <br />
|-<br />
|align="center" | 1 || smooth backbone passing through ribose C3' atoms, backbone terminates at last C3' on either end of chain<br />
|-<br />
|align="center" | 2 || smooth backbone passing through phosphorus atoms, backbone terminates at last phosphorus on 5' end and O3' on 3' end (note takes O3' colour at terminus in default colouring)<br />
|-<br />
|align="center" | 3 || appears same as mode 0<br />
|-<br />
|align="center" | 4 || appears same as mode 2?<br />
|-<br />
|align="center" | 5+ || appears to defult to nucleic acid mode 0<br />
|}<br />
==== Note ====<br />
Note that in ring mode 0 or ring finder 2 the stick projects from the backbone at a point midway between phosphates<br />
<pre>set ribbon_nucleic_acid_mode, value</pre><br />
{|<br />
! align="center" |xxx !! value !! align="left" | effect<br />
|-<br />
|align="center" | ribbon_nucleic_acid_mode || align="center" | integer || has the equivalent behaviour to cartoon_nucleic_acid_mode<br />
|}<br />
<br />
=== Other settings for nucleic acid ===<br />
<pre>set cartoon_nucleic_acid_xxx, value</pre><br />
{|<br />
! xxx !! value !! align="left" | effect<br />
|-<br />
|align="center" | color || color || backbone colour (default is backbone atom colour)<br />
|}</div>Aflaushttps://pymolwiki.org/index.php?title=Overview_of_nucleic_acid_cartoons&diff=4503Overview of nucleic acid cartoons2007-12-09T18:22:59Z<p>Aflaus: </p>
<hr />
<div>== Overview ==<br />
<br />
Pymol has a complex group of settings for controlling the way nucleic acids are represented, broadly separated into:<br />
* ring, for ribose and base ring(s)<br />
* ladder, for the sticks connecting the backbone, ribose and base ring(s)<br />
* nucleic acid, for the smooth backbone path<br />
<br />
Each setting can be altered with the set command. The cartoon settings affect each other so experimentation may be necessary to achieve what you want. Many of the mode settings only seem to work at the global level and cannot be applied to individual objects or selections.<br />
<br />
== Ring settings ==<br />
<br />
=== Ring mode ===<br />
<br />
Ring mode defines the representation of the ribose and base.<br />
<pre>set cartoon_ring_mode, value</pre><br />
{|<br />
!value !!align="left"| effect<br />
|-<br />
|align="center" | 0 || stick from backbone atom to N1 of purines and N3 of pyrimidines<br />
|-<br />
|align="center" | 1 || simple plane for ribose and base rings covering area between ring bonds<br />
|-<br />
|align="center" | 2 || simple plane for ribose and base rings covering area inside sticks (slightly smaller than mode 1)<br />
|-<br />
|align="center" | 3 || plane bounded by sticks for ribose and base rings<br />
|-<br />
|align="center" | 4 || large sphere of ring diameter at centre of ribose and each base ring<br />
|-<br />
|align="center" | 5 || small sphere of 1/10 diameter at centre of ribose and each base ring<br />
|-<br />
|align="center" | 6+ || appears to default to ring mode 2<br />
|}<br />
=== Ring finder ===<br />
<br />
Ring finder defines the rings which are recognised<br />
<pre>set cartoon_ring_finder, value</pre><br />
{|<br />
!value !! align="left" | effect<br />
|-<br />
|align="center" | 0 || no rings or sticks joining them<br />
|-<br />
|align="center" | 1 || both ribose and base ring<br />
|-<br />
|align="center" | 2 || only base ring(s), stick connects directly from phosphate to ring<br />
|-<br />
|align="center" | 3 || very similar to ring finder 1, slight effect on transparency = distinct behaviour?<br />
|-<br />
|align="center" | 4 || very similar to ring finder 1, slight effect on transparency = distinct behaviour?<br />
|-<br />
|align="center" | 5 || sticks visible but rings invisible<br />
|-<br />
|align="center" | 6+ || appears to default to ring finder 5<br />
|}<br />
<br />
=== Other settings for ring ===<br />
<pre>set cartoon_ring_xxx, value</pre><br />
{|<br />
! align="center" | xxx !! value !! align="left" | effect<br />
|-<br />
|align="center" | color || align="center" |color || set the colour of the ring or sphere<br />
|-<br />
|align="center" | width || align="center" | float || thickness of ring for planes and sticks (modes 1, 2, 3)<br />
|-<br />
|align="center" | radius || align="center" |float || radius of ring for spheres (modes 4, 5), negative number gives sphere of same radius as ring in mode 4, approx 1/10 ring diameter in mode 5<br />
|-<br />
|align="center" | transparency || align="center" |float || transparency of ring or sphere, does not affect sticks in ring mode 3<br />
|}<br />
<br />
== Ladder settings ==<br />
<br />
=== Ladder mode ===<br />
<br />
Ladder mode affects the sticks connecting the backbone to ribose and ribose to base, and ring mode 0 or ring finder 5.<br />
<pre>set cartoon_ladder_mode, value</pre><br />
{|<br />
!value !! align="left" | effect<br />
|-<br />
|align="center" | 0 || no sticks shown<br />
|-<br />
|align="center" | 1 || sticks show<br />
|-<br />
|align="center" | 2+ || appears to default to ladder mode 1<br />
|}<br />
=== Other settings for ladder ===<br />
<pre>set cartoon_ladder_xxx, value</pre><br />
{|<br />
! align="center" | xxx !! value !! align="left" | effect<br />
|-<br />
|align="center" | color || color || colour of the stick<br />
|-<br />
|align="center" | radius || float || stick width for ring modes 1, 4 and 5 (default is 0.25), in other ring modes the ladder stick width is controlled by the ring width instead<br />
|}<br />
<br />
== Nucleic acid settings ==<br />
<br />
=== Nucleic acid mode ===<br />
<pre>set cartoon_nucleic_acid_mode, value</pre><br />
{|<br />
!value !! align="left" | effect<br />
|-<br />
|align="center" |0 || smooth backbone passing through phosphorus atoms, backbone terminates at last phosphorus on either end of chain <br />
|-<br />
|align="center" | 1 || smooth backbone passing through ribose C3' atoms, backbone terminates at last C3' on either end of chain<br />
|-<br />
|align="center" | 2 || smooth backbone passing through phosphorus atoms, backbone terminates at last phosphorus on 5' end and O3' on 3' end (note takes O3' colour at terminus in default colouring)<br />
|-<br />
|align="center" | 3 || appears same as mode 0<br />
|-<br />
|align="center" | 4 || appears same as mode 2?<br />
|-<br />
|align="center" | 5+ || appears to defult to nucleic acid mode 0<br />
|}<br />
==== Note ====<br />
Note that in ring mode 0 or ring finder 2 the stick projects from the backbone at a point midway between phosphates<br />
<pre>set ribbon_nucleic_acid_mode, value</pre><br />
{|<br />
! align="center" |xxx !! value !! align="left" | effect<br />
|-<br />
|align="center" | ribbon_nucleic_acid_mode || align="center" | integer || has the equivalent behaviour to cartoon_nucleic_acid_mode<br />
|}<br />
<br />
=== Other settings for nucleic acid ===<br />
<pre>set cartoon_nucleic_acid_xxx, value</pre><br />
{|<br />
! xxx !! value !! align="left" | effect<br />
|-<br />
|align="center" | color || color || backbone colour (default is backbone atom colour)<br />
|}</div>Aflaushttps://pymolwiki.org/index.php?title=Overview_of_nucleic_acid_cartoons&diff=4502Overview of nucleic acid cartoons2007-12-09T17:48:18Z<p>Aflaus: New page: == Overview == Pymol has a complex group of settings for controlling the way nucleic acids are represented, broadly separated into: * ring, for ribose and base ring(s) * ladder, for the s...</p>
<hr />
<div>== Overview ==<br />
<br />
Pymol has a complex group of settings for controlling the way nucleic acids are represented, broadly separated into:<br />
* ring, for ribose and base ring(s)<br />
* ladder, for the sticks connecting the backbone, ribose and base ring(s)<br />
* nucleic acid, for the smooth backbone path<br />
<br />
Each setting can be altered with the set command, for example:<br />
<pre>set cartoon_ring_mode, 1</pre><br />
<br />
The cartoon settings affect each other so experimentation may be necessary to achieve what you want. many of the mode settings only seem to work at the global level and cannot be applied to individual objects or selections.<br />
<br />
== Ring settings ==<br />
<br />
=== Ring mode ===<br />
<br />
Ring mode defines the representation of the ribose and base.<br />
<br />
{|<br />
!cartoon_ring_mode !! align="left" | effect<br />
|-<br />
|align="center" | 0 || stick from backbone atom to N1 of purines and N3 of pyrimidines<br />
|-<br />
|align="center" | 1 || simple plane for ribose and base rings covering area between ring bonds<br />
|-<br />
|align="center" | 2 || simple plane for ribose and base rings covering area inside sticks (slightly smaller than mode 1)<br />
|-<br />
|align="center" | 3 || plane bounded by sticks for ribose and base rings<br />
|-<br />
|align="center" | 4 || large sphere of ring diameter at centre of ribose and each base ring<br />
|-<br />
|align="center" | 5 || small sphere of 1/10 diameter at centre of ribose and each base ring<br />
|-<br />
|align="center" | 6+ || appears to default to ring mode 2<br />
|}<br />
=== Ring finder ===<br />
<br />
Ring finder defines the rings which are recognised<br />
<br />
{|<br />
!cartoon_ring_finder !! align="left" | effect<br />
|-<br />
|align="center" | 0 || no rings or sticks joining them<br />
|-<br />
|align="center" | 1 || both ribose and base ring<br />
|-<br />
|align="center" | 2 || only base ring(s), stick connects directly from phosphate to rin<br />
|-<br />
|align="center" | 3 || very similar to ring finder 1, slight effect on transparency = distinct behaviour?<br />
|-<br />
|align="center" | 4 || very similar to ring finder 1, slight effect on transparency = distinct behaviour?<br />
|-<br />
|align="center" | 5 || sticks visible but rings invisible<br />
|-<br />
|align="center" | 6+ || appears to default to ring finder 5<br />
|}<br />
<br />
==== Other settings for rings ====<br />
<br />
{|<br />
|cartoon_ring_color || color || set the colour of the ring or sphere<br />
|-<br />
|cartoon_ring_width || float || thickness of ring for planes and sticks (modes 1, 2, 3)<br />
|-<br />
|cartoon_ring_radius || float || radius of ring for spheres (modes 4, 5), negative number gives sphere of same radius as ring for mode 4, approx 1/10 ring diameter mode 5<br />
|-<br />
|cartoon_ring_transparency || float || transparency of ring or sphere, does not affect sticks in ring mode 3<br />
|}<br />
<br />
=== Ladder settings ===<br />
<br />
==== Ladder mode ====<br />
<br />
Ladder mode affects the sticks connecting the backbone to ribose and ribose to base, and ring mode 0 or ring finder 5.<br />
<br />
cartoon_ladder_mode 0 no sticks shown<br />
cartoon_ladder_mode 1 sticks shown<br />
cartoon_ladder_mode 2+ appears to default to ladder mode 1<br />
<br />
==== Other settings for ladder ====<br />
<br />
cartoon_ladder_color color colour of the stick<br />
cartoon_ladder_radius float stick width for ring modes 1, 4 and 5 (default is 0.25), in other ring modes the ladder stick width is controlled by the ring width instead<br />
<br />
=== Nucleic acid settings ===<br />
<br />
==== Nucleic acid mode ====<br />
<br />
cartoon_nucleic_acid_mode 0 smooth backbone passing through phosphorus atoms, backbone terminates at last phosphorus on either end of chain <br />
cartoon_nucleic_acid_mode 1 smooth backbone passing through ribose C3' atoms, backbone terminates at last C3' on either end of chain<br />
cartoon_nucleic_acid_mode 2 smooth backbone passing through phosphorus atoms, backbone terminates at last phosphorus on 5' end and O3' on 3' end (note takes O3' colour at terminus in default colouring) <br />
cartoon_nucleic_acid_mode 3 appears same as mode 0?<br />
cartoon_nucleic_acid_mode 4 appears same as mode 2?<br />
cartoon_nucleic_acid_mode 5+ appears to defult to nucleic acid mode 0<br />
ribbon_nucleic_acid_mode has the equivalent behaviour to cartoon_nucleic_acid_mode<br />
<br />
==== Other settings for nucleic acid ====<br />
<br />
cartoon_nucleic_acid_color color backbone colour (default is backbone atom colour)</div>Aflaushttps://pymolwiki.org/index.php?title=Cartoon&diff=4501Cartoon2007-12-09T16:59:15Z<p>Aflaus: /* Other Nucleic Acids & Cartoon Settings */</p>
<hr />
<div>==Cartoon Command==<br />
===DESCRIPTION===<br />
'''cartoon''' changes the default cartoon for a set of atoms.<br />
<br />
===USAGE===<br />
cartoon type, (selection)<br />
<br />
type = skip | automatic | loop | rectangle | oval | tube | arrow | dumbbell<br />
<br />
===PYMOL API===<br />
<source lang="python"><br />
cmd.cartoon(string type, string selection )<br />
</source><br />
<br />
===EXAMPLES===<br />
cartoon rectangle,(chain A)<br />
cartoon skip,(resi 145:156)<br />
<br />
===NOTES===<br />
the "automatic" mode utilizes ribbons according to the information in the PDB HELIX and SHEET records.<br />
<br />
==Adjusting width of cartoon==<br />
Try varying the following.<br />
<br />
For &beta;-strands:<br />
<source lang="python"><br />
cartoon_rect_length<br />
cartoon_rect_width<br />
</source><br />
<br />
For &alpha;-helices:<br />
<source lang="python"><br />
cartoon_oval_length<br />
cartoon_oval_width<br />
</source><br />
<br />
For loops:<br />
<source lang="python"><br />
cartoon_loop_radius<br />
</source><br />
<br />
For "fancy" &alpha;-helices:<br />
<source lang="python"><br />
cartoon_dumbell_length<br />
cartoon_dumbell_width<br />
cartoon_dumbell_radius (radius of cylinder at edge of helix ribbon)<br />
</source><br />
<br />
In each case "length" refers to what some might call the width and "width" refers to what some might call the thickness.<br />
<br />
<br />
[[Image:Cartoon_ex.png|thumb|center|Cartoon Representation Example|300px]]<br />
<br />
<br />
===Forcing Exact Boundaries in Coloring Secondary Structures===<br />
To force PyMol to respect secondary structural elements color-wise (PyMol smooths out colors near color chagnes for a prettier image) use the following <br />
PyMol command:<br />
<code><br />
set cartoon_discrete_colors, on<br />
</code><br />
<br />
[[Image:Cartoon_discrete_color0.png|Discrete Coloring Off|center|thumb]] [[Image:Cartoon_discrete_color1.png|Discrete Coloring On|center|thumb]]<br />
<br />
== Sausage Representation ==<br />
The familiar sausage representation in PyMol is called, "putty". To enable the putty/sausage view simply do,<br />
show cartoon<br />
cartoon putty<br />
unset cartoon_smooth_loops<br />
unset cartoon_flat_sheets<br />
<br />
As of v 0.98 or so, there's a Putty option. Use this.<br />
<br />
[[Image:B_factor_putty.png|thumb|Example of B-factor Putty|center|250px]]<br />
<br />
==Black and White Representation==<br />
'''UPDATE''': This method is essentially obseleted by the new setting '''set ray_trace_mode,2'''. More information on this at [[Ray]].<br />
For those who want a nifty black and white representation of their protein try the following:<br />
# Ray trace your protein of choice in a cartoon representation use a BLACK background<br />
# Save the image<br />
# Load the image in GIMP. [[Image:Bw1.jpeg|thumb|Black BG Ribbon|center|350px]]<br />
# Desaturate or Grayscale the image. [[Image:Bw2.jpeg|thumb|Grayscale|center|350px]]<br />
# Run the filter: Filter->Edge-Detect->Edge. [[Image:Bw3.jpeg|thumb|Edge Detect|center|350px]]<br />
# Select: Layers->Color->Invert. [[Image:Bw4.jpeg|thumb|Invert Color|center|350px]]<br />
# Different methods of edge detection will give you different results. In the last example, I used Laplace Edge-Detect, then painted an all white layer beneath the current layer to achieve the results. [[Image:Bw5.jpeg|thumb|Other Styles|center|350px|Comments]]<br />
<br />
<br />
I'm sure there are other ways to do this. If you want to include it in a publication make sure you ray traced it large enough. For that, see [[:Category:Advanced_Issues_Image_Manipulation_Publication_Quatlity_Images|Creating Publication Quality Images]].<br />
<br />
==CA (Alpha Carbon) Trace==<br />
If you have a structure with just a alpha carbon trace, you can get a cartoon by<br />
<source lang="python"><br />
set cartoon_trace,1<br />
show cartoon<br />
</source><br />
If your structure is more than just the CA backbone, the cartoon representation will look incorrect, so use it just with CA trace.<br />
<br />
==Various Transparency Levels==<br />
[[Image:Cartoon_multi_transp.png|thumb|center|Example of Cartoon Multi-level Transparency. The near cartoon has transparency setting '''0.2''', the segment in the BG '''0.5'''.]]<br />
One can make different cartoon selections have different transparency values, in PyMol. The trick here is to use "create" instead of "select". Create makes new objects that can have independent settings. <br />
<br />
<source lang="python"><br />
load mol_obj.pdb<br />
<br />
# transfer a piece of the molecule into a new object<br />
<br />
create new_obj, chain A<br />
remove mol_obj in new_obj<br />
<br />
# adjust trasparency for the new object<br />
<br />
set cartoon_transparency, 0.5, new_obj<br />
</source><br />
<br />
== Nucleic Acid Representation ==<br />
[[Image:Nucleic1.png|thumb|center|Showing Nucleic Acids]]<br />
To show nucleic acids in a nicer format do:<br />
<source lang="python"><br />
set cartoon_ring_mode,1<br />
show cartoon<br />
</source><br />
<br />
=== Other Nucleic Acids & Cartoon Settings ===<br />
Here are some things to try:<br />
<source lang="python"><br />
set cartoon_ring_mode, 1 # (or 2 or 3)<br />
set cartoon_ring_finder, 1 # (or 2 or 3 or 4)<br />
set cartoon_nucleic_acid_mode, 0 # (or 1 or 2 or 3 or 4)<br />
<br />
set cartoon_side_chain_helper<br />
rebuild<br />
<br />
set cartoon_ring_transparency, 0.5<br />
<br />
set cartoon_ladder_mode, 0 # or 1<br />
<br />
set cartoon_ladder_color, color-name<br />
set cartoon_nucleic_acid_color, color-name<br />
<br />
cartoon oval<br />
set cartoon_oval_width, 0.8<br />
<br />
cartoon rect<br />
<br />
cartoon dumbbell<br />
set cartoon_dumbbell_width, 0.4<br />
set cartoon_dumbbell_radius, 0.4<br />
</source><br />
[[Nucleic acid cartoon settings]]<br />
<br />
[[Examples of nucleic acid cartoons]]<br />
<br />
== See Also ==<br />
[[Displaying_Biochemical_Properties]]<br />
<br />
[[Category:Representations|Cartoon]]<br />
[[Category:Nucleic_Acids|Cartoon]]</div>Aflaushttps://pymolwiki.org/index.php?title=Cartoon&diff=4500Cartoon2007-12-09T16:58:11Z<p>Aflaus: /* Other Nucleic Acids & Cartoon Settings */</p>
<hr />
<div>==Cartoon Command==<br />
===DESCRIPTION===<br />
'''cartoon''' changes the default cartoon for a set of atoms.<br />
<br />
===USAGE===<br />
cartoon type, (selection)<br />
<br />
type = skip | automatic | loop | rectangle | oval | tube | arrow | dumbbell<br />
<br />
===PYMOL API===<br />
<source lang="python"><br />
cmd.cartoon(string type, string selection )<br />
</source><br />
<br />
===EXAMPLES===<br />
cartoon rectangle,(chain A)<br />
cartoon skip,(resi 145:156)<br />
<br />
===NOTES===<br />
the "automatic" mode utilizes ribbons according to the information in the PDB HELIX and SHEET records.<br />
<br />
==Adjusting width of cartoon==<br />
Try varying the following.<br />
<br />
For &beta;-strands:<br />
<source lang="python"><br />
cartoon_rect_length<br />
cartoon_rect_width<br />
</source><br />
<br />
For &alpha;-helices:<br />
<source lang="python"><br />
cartoon_oval_length<br />
cartoon_oval_width<br />
</source><br />
<br />
For loops:<br />
<source lang="python"><br />
cartoon_loop_radius<br />
</source><br />
<br />
For "fancy" &alpha;-helices:<br />
<source lang="python"><br />
cartoon_dumbell_length<br />
cartoon_dumbell_width<br />
cartoon_dumbell_radius (radius of cylinder at edge of helix ribbon)<br />
</source><br />
<br />
In each case "length" refers to what some might call the width and "width" refers to what some might call the thickness.<br />
<br />
<br />
[[Image:Cartoon_ex.png|thumb|center|Cartoon Representation Example|300px]]<br />
<br />
<br />
===Forcing Exact Boundaries in Coloring Secondary Structures===<br />
To force PyMol to respect secondary structural elements color-wise (PyMol smooths out colors near color chagnes for a prettier image) use the following <br />
PyMol command:<br />
<code><br />
set cartoon_discrete_colors, on<br />
</code><br />
<br />
[[Image:Cartoon_discrete_color0.png|Discrete Coloring Off|center|thumb]] [[Image:Cartoon_discrete_color1.png|Discrete Coloring On|center|thumb]]<br />
<br />
== Sausage Representation ==<br />
The familiar sausage representation in PyMol is called, "putty". To enable the putty/sausage view simply do,<br />
show cartoon<br />
cartoon putty<br />
unset cartoon_smooth_loops<br />
unset cartoon_flat_sheets<br />
<br />
As of v 0.98 or so, there's a Putty option. Use this.<br />
<br />
[[Image:B_factor_putty.png|thumb|Example of B-factor Putty|center|250px]]<br />
<br />
==Black and White Representation==<br />
'''UPDATE''': This method is essentially obseleted by the new setting '''set ray_trace_mode,2'''. More information on this at [[Ray]].<br />
For those who want a nifty black and white representation of their protein try the following:<br />
# Ray trace your protein of choice in a cartoon representation use a BLACK background<br />
# Save the image<br />
# Load the image in GIMP. [[Image:Bw1.jpeg|thumb|Black BG Ribbon|center|350px]]<br />
# Desaturate or Grayscale the image. [[Image:Bw2.jpeg|thumb|Grayscale|center|350px]]<br />
# Run the filter: Filter->Edge-Detect->Edge. [[Image:Bw3.jpeg|thumb|Edge Detect|center|350px]]<br />
# Select: Layers->Color->Invert. [[Image:Bw4.jpeg|thumb|Invert Color|center|350px]]<br />
# Different methods of edge detection will give you different results. In the last example, I used Laplace Edge-Detect, then painted an all white layer beneath the current layer to achieve the results. [[Image:Bw5.jpeg|thumb|Other Styles|center|350px|Comments]]<br />
<br />
<br />
I'm sure there are other ways to do this. If you want to include it in a publication make sure you ray traced it large enough. For that, see [[:Category:Advanced_Issues_Image_Manipulation_Publication_Quatlity_Images|Creating Publication Quality Images]].<br />
<br />
==CA (Alpha Carbon) Trace==<br />
If you have a structure with just a alpha carbon trace, you can get a cartoon by<br />
<source lang="python"><br />
set cartoon_trace,1<br />
show cartoon<br />
</source><br />
If your structure is more than just the CA backbone, the cartoon representation will look incorrect, so use it just with CA trace.<br />
<br />
==Various Transparency Levels==<br />
[[Image:Cartoon_multi_transp.png|thumb|center|Example of Cartoon Multi-level Transparency. The near cartoon has transparency setting '''0.2''', the segment in the BG '''0.5'''.]]<br />
One can make different cartoon selections have different transparency values, in PyMol. The trick here is to use "create" instead of "select". Create makes new objects that can have independent settings. <br />
<br />
<source lang="python"><br />
load mol_obj.pdb<br />
<br />
# transfer a piece of the molecule into a new object<br />
<br />
create new_obj, chain A<br />
remove mol_obj in new_obj<br />
<br />
# adjust trasparency for the new object<br />
<br />
set cartoon_transparency, 0.5, new_obj<br />
</source><br />
<br />
== Nucleic Acid Representation ==<br />
[[Image:Nucleic1.png|thumb|center|Showing Nucleic Acids]]<br />
To show nucleic acids in a nicer format do:<br />
<source lang="python"><br />
set cartoon_ring_mode,1<br />
show cartoon<br />
</source><br />
<br />
=== Other Nucleic Acids & Cartoon Settings ===<br />
Here are some things to try:<br />
<source lang="python"><br />
set cartoon_ring_mode, 1 # (or 2 or 3)<br />
set cartoon_ring_finder, 1 # (or 2 or 3 or 4)<br />
set cartoon_nucleic_acid_mode, 0 # (or 1 or 2 or 3 or 4)<br />
<br />
set cartoon_side_chain_helper<br />
rebuild<br />
<br />
set cartoon_ring_transparency, 0.5<br />
<br />
set cartoon_ladder_mode, 0 # or 1<br />
<br />
set cartoon_ladder_color, color-name<br />
set cartoon_nucleic_acid_color, color-name<br />
<br />
cartoon oval<br />
set cartoon_oval_width, 0.8<br />
<br />
cartoon rect<br />
<br />
cartoon dumbbell<br />
set cartoon_dumbbell_width, 0.4<br />
set cartoon_dumbbell_radius, 0.4<br />
</source><br />
[[Examples of nucleic acid cartoons]]<br />
<br />
== See Also ==<br />
[[Displaying_Biochemical_Properties]]<br />
<br />
[[Category:Representations|Cartoon]]<br />
[[Category:Nucleic_Acids|Cartoon]]</div>Aflaushttps://pymolwiki.org/index.php?title=Talk:Examples_of_cartoon_ring_and_cartoon_ladder_settings&diff=4499Talk:Examples of cartoon ring and cartoon ladder settings2007-12-09T16:57:10Z<p>Aflaus: Talk:Examples of cartoon ring and cartoon ladder settings moved to Talk:Examples of nucleic acid cartoons</p>
<hr />
<div>#REDIRECT [[Talk:Examples of nucleic acid cartoons]]</div>Aflaushttps://pymolwiki.org/index.php?title=Examples_of_cartoon_ring_and_cartoon_ladder_settings&diff=4497Examples of cartoon ring and cartoon ladder settings2007-12-09T16:57:09Z<p>Aflaus: Examples of cartoon ring and cartoon ladder settings moved to Examples of nucleic acid cartoons</p>
<hr />
<div>#REDIRECT [[Examples of nucleic acid cartoons]]</div>Aflaushttps://pymolwiki.org/index.php?title=Examples_of_nucleic_acid_cartoons&diff=4496Examples of nucleic acid cartoons2007-12-09T16:57:09Z<p>Aflaus: Examples of cartoon ring and cartoon ladder settings moved to Examples of nucleic acid cartoons</p>
<hr />
<div>== pymol version info ==<br />
The various new nucleic acid display settings for PyMol 0.99 listed below were produced using version 0.99 beta 29 on Windows XP with an arbitrary B-form DNA molecule. Higher values could be set for each setting but appeared to yield the default representations.<br />
== default settings ==<br />
The defaults give a phosphate backbone with single sticks passing across the full width of the base plane.<br />
<source lang="python"><br />
set cartoon_nucleic_acid_mode, 1 # backbone follows phosphates<br />
set cartoon_ladder_mode, 1 # sticks from backbone into nucleotide<br />
set cartoon_ring_mode, 0 # no nucleotide rings<br />
set cartoon_ring_finder, 1 # ribose and base rings (not displayed as ring mode 0)<br />
</source><br />
{|<br />
|[[Image:DNAcartoon_ringmode0_laddermode1_ringfinder1_nucleicacidmode0.png|default view|thumb]]<br />
|}<br />
== cartoon ring modes ==<br />
<source lang="python"><br />
set cartoon_ring_mode, 0 # no nucleotide rings<br />
set cartoon_ring_mode, 1 # filled rings extending to outside edge of bonds<br />
set cartoon_ring_mode, 2 # filled rings extending to inside edge of bonds<br />
set cartoon_ring_mode, 3 # filled rings with bonds as thicker lines<br />
</source><br />
{|<br />
|[[Image:DNAcartoon_ringmode0_laddermode1_ringfinder1_nucleicacidmode0.png|cartoon_ring_mode,0|thumb]]<br />
|[[Image:DNAcartoon_ringmode1_laddermode1_ringfinder1_nucleicacidmode0.png|cartoon_ring_mode,1|thumb]]<br />
|[[Image:DNAcartoon_ringmode2_laddermode1_ringfinder1_nucleicacidmode0.png|cartoon_ring_mode,2|thumb]]<br />
|[[Image:DNAcartoon_ringmode3_laddermode1_ringfinder1_nucleicacidmode0.png|cartoon_ring_mode,3|thumb]]<br />
|}<br />
<center>all with defaults:&nbsp;<i>cartoon_ladder_mode,1&nbsp;&nbsp;&nbsp;cartoon_nucleic_acid_mode,0&nbsp;&nbsp;&nbsp;cartoon_ring_finder,1</i></center><br />
== cartoon ladder modes ==<br />
<source lang="python"><br />
set cartoon_ladder_mode, 0 # no ladder<br />
set cartoon_ladder_mode, 1 # with ladder, as stick (if ring mode 0) or link to ring (if rings)<br />
</source><br />
note that the visibility of the ladder sticks depends on ring mode >0, ring finder >0, nucleic acid mode = 0<br />
{|<br />
|[[Image:DNAcartoon_ringfinder1_ringmode3_laddermode0_nucleicacidmode0.png|cartoon_ladder_mode,0|thumb]]<br />
|[[Image:DNAcartoon_ringfinder3_ringmode3_laddermode1_nucleicacidmode0.png|cartoon_ladder_mode,1|thumb]]<br />
|}<br />
all with:&nbsp;<i>cartoon_ring_mode,3&nbsp;&nbsp;&nbsp;cartoon_nucleic_acid_mode,0&nbsp;&nbsp;&nbsp;cartoon_ring_finder,1</i><br />
== cartoon nucleic acid modes ==<br />
<source lang="python"><br />
set cartoon_nucleic_acid_mode, 0 # backbone follow phosphates (red)<br />
set cartoon_nucleic_acid_mode, 1 # backbone follows C4' of ribose (green)<br />
</source><br />
{|<br />
|[[Image:DNAcartoon_ringfinder1_ringmode3_laddermode0_nucleicacidmode0.png|cartoon_nucleic_acid_mode,0|thumb]]<br />
|[[Image:DNAcartoon_ringfinder1_ringmode3_laddermode0_nucleicacidmode1.png|cartoon_nucleic_acid_mode,1|thumb]]<br />
|}<br />
all with:&nbsp;<i>cartoon_ladder_mode,0&nbsp;&nbsp;&nbsp;cartoon_ring_mode,3&nbsp;&nbsp;&nbsp;cartoon_ring_finder,1</i><br />
== cartoon ring finder ==<br />
<source lang="python"><br />
set cartoon_ring_finder, 0 # no ribose, base (or ladder)<br />
set cartoon_ring_finder, 1 # ribose and base ring<br />
set cartoon_ring_finder, 2 # base ring only<br />
</source><br />
{|<br />
|[[Image:DNAcartoon_ringfinder0_ringmode3_laddermode1_nucleicacidmode0.png|cartoon_ring_finder,0|thumb]]<br />
|[[Image:DNAcartoon_ringfinder1_ringmode3_laddermode1_nucleicacidmode0.png|cartoon_ring_finder,1|thumb]]<br />
|[[Image:DNAcartoon_ringfinder2_ringmode3_laddermode1_nucleicacidmode0.png|cartoon_ring_finder,2|thumb]]<br />
|}<br />
all with:&nbsp;<i>cartoon_ladder_mode,1&nbsp;&nbsp;&nbsp;cartoon_ring_mode,3&nbsp;&nbsp;&nbsp;cartoon_nucleic_acid_mode,0</i><br />
<br />
[[Category:Nucleic_Acids|Cartoon ring and cartoon ladder settings]]</div>Aflaushttps://pymolwiki.org/index.php?title=MAC_Install&diff=4491MAC Install2007-12-08T19:16:17Z<p>Aflaus: /* Install pymol with Fink */</p>
<hr />
<div>[[Category:Installation|Mac]]<br />
http://images.apple.com/powermac/images/solutionsscience20050427.jpg<br />
<br />
__TOC__<br />
<br />
=Installing MacPyMOL=<br />
http://delsci.com/macpymol/macpymol350.jpg<br />
<br />
===Essentials===<br />
<br />
The [http://delsci.com/macpymol/ download] is about as straightforward as it gets, and you can install it wherever it makes you happy. You need a 3 button mouse (clickable scroll wheel = middle button). Apple has finally come to its senses and designed a proper, ergonomically pleasant, [http://www.apple.com/mightymouse/ scrollbutton mouse] that works well with pymol and permits horizontal scrolling. Most other mice will also work well.<br />
<br />
===Warning on Mouse Drivers===<br />
<br />
One word of warning: '''Do not install 3rd party drivers''' for multi-button mice if you can avoid it. These often mess with the mapping of the middle button or have other horrific side effects. Fortunately, with OS X, you should not need to.<br />
<br />
===Invoking pymol from the unix command line===<br />
<br />
The unix executable resides at MacPyMOL.app/Contents/MacOS/MacPyMOL<br />
<br />
I ([[User:Wgscott|Bill Scott]]) wrote a cheezy [http://xanana.ucsc.edu/Library/init/zsh/local-functions/xtal/pymol pymol] shell script (and zsh function) to invoke this on the command line. It uses mdfind to find the executable. I also use [[MacOSX-specific .pymolrc file|this ~/.pymolrc]] file.<br />
<br />
Additional invokation options and further details are discussed under [[Launching_PyMOL#MacOS_X:]]<br />
<br />
===Extras===<br />
<br />
You don't need any of these to use MacPyMOL. But you didn't really '''need''' a Mac either. Face it: You need these.<br />
<br />
====Mighty Mouse====<br />
<br />
http://images.apple.com/mightymouse/images/index360scroll220050802.gif<br />
<br />
A 3-button mouse is essential. [http://www.apple.com/mightymouse/ Apple's Mighty Mouse] is an extra treat.<br />
<br />
====PowerMate Dial====<br />
<br />
http://www.griffintechnology.com/assets/images/products/powermate/prod_powermate_sub01b.jpg<br />
<br />
The [http://www.chemistry.ucsc.edu/~wgscott/xtal/powermate_pymol_osx.html PowerMate dial works nicely with pymol].<br />
<br />
====Stereo====<br />
<br />
http://images.apple.com/powermac/images/graphicspymol20051018.jpg<br />
<br />
The [http://www.apple.com/powermac/upgrade.html latest Macs] finally support [http://www.apple.com/powermac/graphics.html stereo in a window]. There is more information in the [[Monitors Hardware Options]] section.<br />
<br />
====Second Monitor====<br />
The trick to getting MacPyMOL to work in stereo on the second monitor is to force it to initially open on that display by providing an appropriate "-X #" (and perhaps -Y #) option on launch. That way the OpenGL context will be created with stereo support.<br />
<source lang="python"><br />
./MacPyMOL.app/Contents/MacOS/MacPyMOL -X -1000<br />
./MacPyMOL.app/Contents/MacOS/MacPyMOL -X -1000 -Y 100<br />
</source><br />
<br />
'''Source:''' ''Warren DeLano; PyMOL Users Archive''<br />
<br />
=Installing X-windows based pymol on Mac OS X=<br />
<br />
===Why would you want to do this?===<br />
<br />
#You want to run a [http://www.oreilly.com/openbook/freedom/ free], guilt-free, open-source version of pymol<br />
#You just happen to prefer the [http://wiki.python.org/moin/TkInter tkinter] menu<br />
#You want to use [http://pymol.sourceforge.net/plugins.html plugins], for example, the [http://www-personal.umich.edu/~mlerner/PyMOL/ apbs plugin] for free grasp-like electrostatic calculations.<br />
<br />
----<br />
<br />
===Simplest Installation===<br />
<br />
====Install pymol with Fink====<br />
http://pdb.finkproject.org/img/mlogo.png<br />
<br />
By far the simplest way to install the X-windows based version of pymol on OS X is by using the [http://fink.sourceforge.net/ fink package management system]. To compile it, all you need to do is issue the command<br />
<br />
fink install pymol-py25<br />
<br />
(This will install python2.5 in fink, along with an X-windows based tkinter. There are also versions that permit you to install pymol to interact with python2.4 and even python2.3. Fink uses its own unix-type python installation.)<br />
<br />
The [http://pdb.finkproject.org/pdb/package.php/pymol-py25 fink pymol package] currently exists in the [http://fink.sourceforge.net/faq/usage-fink.php#unstable unstable branch of fink], so you will either have to [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/How_to_Activate_the_Unstable_Branch activate the unstable branch] or make the following symbolic links:<br />
<br />
sudo ln -s /sw/fink/dists/unstable/main/finkinfo/sci/pymol-py.* /sw/fink/dists/local/main/finkinfo/.<br />
<br />
You might need to create the latter directory if it doesn't already exist, i.e., issue the command<br />
<br />
sudo mkdir -p /sw/fink/dists/local/main/finkinfo<br />
<br />
10.4 ONLY: Be sure to set your display environment in your start up shell script to use pymol. For example in your home directory, the .bashrc (or .bash_profile) file should contain:<br />
<br />
export DISPLAY=":0.0"<br />
<br />
Do NOT set the DISPLAY variable for 10.5, as God does this for you automatically.<br />
<br />
If for some reason you don't want to set DISPLAY, launch X11 manually (Applications/Utilities) then start a login shell with 'xterm -ls' (note default xterm is not a login shell so will not read .bashrc) and finally issue 'pymol' <br />
<br />
Fink pymol also reads ~/.pymolrc in your home directory.<br />
<br />
I ([[User:wgscott|wgscott]]) have put a whole lot of further information on how to use fink to install crystallographic software on my own [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Main_Page wiki] and [http://chemistry.ucsc.edu/~wgscott/xtal/ website], including instructions on [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Getting_your_fink_installation_to_use_packages_that_I_have_pre-compiled how to install precompiled binary packages using fink].<br />
<br />
The [http://pdb.finkproject.org/pdb/search.php?summary=pymol fink pymol package] is currently maintained by Jack Howarth.<br />
<br />
====Install APBS and friends with fink====<br />
<br />
[[Image:Rna_surface_apbs.png|thumb|APBS calculated electrostatic potential of SARS s2m RNA reveals the colors of a true patriot.]]<br />
<br />
To use the electrostatics plugin, you will need [http://apbs.sourceforge.net/ APBS] and its dependencies. These are also available as fink packages, and include [http://pdb.finkproject.org/pdb/package.php/apbs apbs], [http://pdb.finkproject.org/pdb/package.php/maloc maloc] and [http://pdb.finkproject.org/pdb/package.php/pdb2pqr pdb2pqr]. If you have multiple processors available, you might wish to install the [http://pdb.finkproject.org/pdb/package.php/apbs-mpi mpi version of apbs].<br />
<br />
Issuing the command<br />
<br />
fink install apbs<br />
<br />
will install apbs and its required dependencies for you. The fink pymol package is already preconfigured to do the right thing to use apbs as a plugin. Here is [http://xanana.ucsc.edu/xtal/pymol_screenshot.png a big screenshot of the fink APBS package being invoked via the pymol plugin].<br />
<br />
'''Nucleic acids''' may prove problematic for the apbs plugin. If so, use the pdb2pqr command-line tool to create a pqr file manually, instead of using the plugin to generate it.<br />
<br />
----<br />
<br />
<br />
<br />
===PyMOLX11Hybrid=== <br />
<br />
MacPyMOL for Tiger now includes a hybrid X11 mode. Assuming that X11 is already installed, simply duplicate MacPyMOL.app and rename it "PyMOLX11Hybrid.app" and launch.<br />
<br />
<br />
[[Category:Nucleic_Acids|MAC Install]]<br />
[[Category:Technical Issues|MAC Install]]</div>Aflaushttps://pymolwiki.org/index.php?title=Launching_PyMOL&diff=4490Launching PyMOL2007-12-08T19:03:18Z<p>Aflaus: /* Reading the pymolrc file */</p>
<hr />
<div>=Launching PyMOL=<br />
<br />
[[Command Line Options]]<br />
<br />
[[Launching From a Script]]<br />
<br />
==Invoking PyMOL and reading startup commands from a file==<br />
<br />
===<b>Linux:</b>===<br />
Assuming the executable is in your $PATH, simply issue<br />
<br />
pymol<br />
<br />
together with any [[Command Line Options]] and arguments (pdb files, pse files, map files and so forth) you require.<br />
<br />
Whenever PyMol starts, a user-created '~/.pymolrc' file containing commands is run. All you need to do is create ".pymolrc" and place it in your home directory. Alternatively, you can instead create ".pymolrc.py" which contains actual Python code instead of just PyMOL commands.<br />
<br />
===<b>Windows:</b>===<br />
On Windows, use 'pymolrc', 'pymolrc.py' or 'pymolrc.pym'. For global defaults (all users), you can place a .pymolrc file in C:\Program Files\DeLano Scientific\PyMOL<br />
<br />
===<b>MacOS X:</b>===<br />
<br />
====Launching the Application====<br />
You can launch MacPyMOL by <br />
<br />
* Double-clicking the application's icon, or by <br />
<br />
* Issuing the unix command<br />
<br />
open -a MacPyMOL<br />
<br />
or by <br />
<br />
* Directly invoking the unix executable<br />
<br />
/Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL<br />
<br />
The latter assumes the application has been placed in /Applications, so adjust the absolute path if you have it elsewhere. If you directly invoke the unix executable to launch pymol, it has the advantage that you can pass [[Command Line Options]] and arguments to it in the usual way. You might wish to '''make an alias'''<br />
<br />
alias pymol=/Applications/Xtal/MacPyMOL.app/Contents/MacOS/MacPyMOL<br />
<br />
(leave out the equal sign for tcsh) '''or symbolic link'''<br />
<br />
sudo ln -s /Applications/Xtal/MacPyMOL.app/Contents/MacOS/MacPyMOL /usr/local/bin/pymol<br />
<br />
or '''use this shell script''' [[User:Wgscott|I]] wrote: [http://xanana.ucsc.edu/Library/init/zsh/local-functions/xtal/pymol pymol] shell script (and zsh function) to invoke pymol on the command line. It uses OS X 10.4's mdfind to locate the executable.<br />
<br />
* If MacPyMOL is set as the default application to open pdb, pse and other such files, double-clicking any of those files (or issuing the unix open command) will start also pymol and load the file you clicked on.<br />
<br><br />
<br />
====Reading the pymolrc file====<br />
In each case, pymol will read the contents of the user's ~/.pymolrc file and/or ~/.pymolrc.py file (as with Linux). <br />
<br />
Here is one example of a [[MacOSX-specific .pymolrc file]] with a script enabling interaction via the [[MAC_Install#PowerMate_Dial |PowerMate Dial]]<br />
<br />
A couple of simple lines to put in your .pymolrc might be to respectively change to your favourite directory and increase the window size:<br />
<pre><br />
cd ~/Documents/structures/<br />
viewport 750,750<br />
</pre><br />
<br />
==Launching PyMOL from an external application==<br />
<br />
If PYMOL_PATH, LD_LIBRARY_PATH, and TCL_LIBRARY are correctly defined, then you can launch PyMOL from an external Python program as shown in ''examples/devel/start_pymol.py''.<br />
<br />
NOTE: This approach is not recommended, since the PyMOL launching process is subject to change without warning. The recommended approach is to just use PyMOL as your python interpreter:<br />
<source lang="python"><br />
pymol -r <script.py><br />
pymol -qcr <script.py><br />
</source><br />
<br />
<br />
==Running PyMOL in batch mode==<br />
<br />
To perform PyMOL commands from stdin (file, pipe) without opening an OpenGL window, try:<br />
<source lang="python"><br />
pymol -qc<br />
</source><br />
<br />
==Suppressing PyMOL output==<br />
To suppress most of PyMOL's normal chatter, just type on the Cmd line:<br />
<source lang="python"><br />
feedback disable,all,actions<br />
feedback disable,all,results<br />
</source><br />
or, from Python:<br />
<source lang="python"><br />
cmd.feedback("disable","all","actions")<br />
cmd.feedback("disable","all","results")<br />
</source><br />
<br />
<br />
==Launching Python scripts==<br />
Running a Python script from PyMOL, usually the command:<br />
<source lang="python"><br />
run script.py<br />
</source><br />
Is enough. Of course, the file script.py needs to be in the working directory.<br />
For more detailed examples, see the commands to launch Python scripts when starting PyMOL. Asynchronous means, that a new Python thread is started:<br />
<br />
<source lang="python"><br />
pymol example.py # synchronous, in PyMOL module<br />
pymol -r example.py # synchronous in __main__ module<br />
pymol -l example.py # asychronous in a new module<br />
</source><br />
<br />
You can also launch python programs from within PyMOL with the commands:<br />
<source lang="python"><br />
run example.py # synchronous in pymol module<br />
run example.py,main # synchronous in __main__ module<br />
<br />
spawn example.py # asychronous in a new module<br />
spawn example.py,global # asychronous in the PyMOL module<br />
spawn example.py,main # asychronous in the __main__ module<br />
</source><br />
<br />
<br />
==Overwriting Default Settings==<br />
If you don't like the cartoon default color and want to change default settings for it, from green to slate, you add the command line to do this in '''$HOME/.pymolrc'''.<br />
Here, 'set cartoon_color, slate'<br />
<br />
Windows users can do this with a pymolrc file.</div>Aflaushttps://pymolwiki.org/index.php?title=Color_Values&diff=3475Color Values2005-11-19T23:43:00Z<p>Aflaus: </p>
<hr />
<div>==Background==<br />
*Naming<br />
**All listed colours can be specified by name (eg color red, mymolecule)<br />
**American and English spellings of gray/grey and color/colour can be used<br />
*Sources<br />
**Pymol colours are specified as triples of independent Red, Green and Blue contribution in range 0-1.0<br />
**Colour specs from source files Color.c, menu.py and appearance.py of Pymol 0.99 beta29<br />
**Colour names can be defined/redefined using set_color command or interactively in Colors item within Setting menu<br />
==Spectral range colours==<br />
Spectral ranges are available by name including numerical value (eg grey56, s532)<br />
*Grays from 'gray00' to 'gray99' (white to black)<br />
*Spectrum from 's000' to 's999' (violet to red)<br />
*Original spectrum with extra blue and red at ends from 'o000' to 'o999'<br />
*Reversed offset spectrum from 'r000' to 'r999'<br />
*Complementary spectrum from 'c000' to 'c999'<br />
*Complementary spectrum separated by white from 'w000' to 'w999'<br />
See Colour.c in source code for details about how spectra are calculated<br />
==Simple named colours==<br />
{| cellpadding="1"<br />
|- align="center"<br />
!width="20"|&nbsp;||bgcolor=gray width="100"|name||bgcolor=red width="50"|R||bgcolor=green width="50"|G||bgcolor=blue width="50"|B||bgcolor=gray|note<br />
|- align="center"<br />
|bgcolor="#7fffff"|&nbsp;||aquamarine||0.5||1.0||1.0||<br />
|- align="center"<br />
|bgcolor="#000000"|&nbsp;||black||0.0||0.0||0.0||<br />
|- align="center"<br />
|bgcolor="#0000ff"|&nbsp;||blue||0.0||0.0||1.0||<br />
|- align="center"<br />
|bgcolor="#d8d8ff"|&nbsp;||bluewhite||0.85||0.85||1.00||<br />
|- align="center"<br />
|bgcolor="#1919ff"|&nbsp;||br0||0.1||0.1||1.0||<br />
|- align="center"<br />
|bgcolor="#3319e5"|&nbsp;||br1||0.2||0.1||0.9||<br />
|- align="center"<br />
|bgcolor="#4c19cc"|&nbsp;||br2||0.3||0.1||0.8||<br />
|- align="center"<br />
|bgcolor="#6619b2"|&nbsp;||br3||0.4||0.1||0.7||<br />
|- align="center"<br />
|bgcolor="#7f1999"|&nbsp;||br4||0.5||0.1||0.6||<br />
|- align="center"<br />
|bgcolor="#99197f"|&nbsp;||br5||0.6||0.1||0.5||<br />
|- align="center"<br />
|bgcolor="#b21966"|&nbsp;||br6||0.7||0.1||0.4||<br />
|- align="center"<br />
|bgcolor="#cc194c"|&nbsp;||br7||0.8||0.1||0.3||<br />
|- align="center"<br />
|bgcolor="#e51933"|&nbsp;||br8||0.9||0.1||0.2||<br />
|- align="center"<br />
|bgcolor="#ff1919"|&nbsp;||br9||1.0||0.1||0.1||<br />
|- align="center"<br />
|bgcolor="#ffb233"|&nbsp;||brightorange||1.0||0.7||0.2||<br />
|- align="center"<br />
|bgcolor="#a5512b"|&nbsp;||brown||0.65||0.32||0.17||<br />
|- align="center"<br />
|bgcolor="#33ff33"|&nbsp;||carbon||0.2||1.0||0.2||<br />
|- align="center"<br />
|bgcolor="#7fff00"|&nbsp;||chartreuse||0.5||1.0||0.0||AKA puke green<br />
|- align="center"<br />
|bgcolor="#8d381c"|&nbsp;||chocolate||0.555||0.222||0.111||<br />
|- align="center"<br />
|bgcolor="#00ffff"|&nbsp;||cyan||0.0||1.0||1.0||<br />
|- align="center"<br />
|bgcolor="#ba8c84"|&nbsp;||darksalmon||0.73||0.55||0.52||<br />
|- align="center"<br />
|bgcolor="#ffff00"|&nbsp;||dash||1.0||1.0||0.0||<br />
|- align="center"<br />
|bgcolor="#3f3fa5"|&nbsp;||deepblue||0.25||0.25||0.65||deep<br />
|- align="center"<br />
|bgcolor="#999919"|&nbsp;||deepolive||0.6||0.6||0.1||<br />
|- align="center"<br />
|bgcolor="#991999"|&nbsp;||deeppurple||0.6||0.1||0.6||<br />
|- align="center"<br />
|bgcolor="#ff7f7f"|&nbsp;||deepsalmon||1.0||0.5||0.5||duplicated?<br />
|- align="center"<br />
|bgcolor="#ff6b6b"|&nbsp;||deepsalmon||1.00||0.42||0.42||duplicated?<br />
|- align="center"<br />
|bgcolor="#199999"|&nbsp;||deepteal||0.1||0.6||0.6||<br />
|- align="center"<br />
|bgcolor="#191999"|&nbsp;||density||0.1||0.1||0.6||<br />
|- align="center"<br />
|bgcolor="#b27f7f"|&nbsp;||dirtyviolet||0.70||0.50||0.50||<br />
|- align="center"<br />
|bgcolor="#b12121"|&nbsp;||firebrick||0.698||0.13||0.13||<br />
|- align="center"<br />
|bgcolor="#339933"|&nbsp;||forest||0.2||0.6||0.2||<br />
|- align="center"<br />
|bgcolor="#7f7f7f"|&nbsp;||gray||0.5||0.5||0.5||american spelling<br />
|- align="center"<br />
|bgcolor="#00ff00"|&nbsp;||green||0.0||1.0||0.0||<br />
|- align="center"<br />
|bgcolor="#3fffbf"|&nbsp;||greencyan||0.25||1.00||0.75||<br />
|- align="center"<br />
|bgcolor="#7f7f7f"|&nbsp;||grey||0.5||0.5||0.5||english spelling<br />
|- align="center"<br />
|bgcolor="#ff007f"|&nbsp;||hotpink||1.0||0.0||0.5||<br />
|- align="center"<br />
|bgcolor="#e5e5e5"|&nbsp;||hydrogen||0.9||0.9||0.9||<br />
|- align="center"<br />
|bgcolor="#bfbfff"|&nbsp;||lightblue||0.75||0.75||1.0||<br />
|- align="center"<br />
|bgcolor="#ff33cc"|&nbsp;||lightmagenta||1.0||0.2||0.8||<br />
|- align="center"<br />
|bgcolor="#ffcc7f"|&nbsp;||lightorange||1.0||0.8||0.5||<br />
|- align="center"<br />
|bgcolor="#ffbfdd"|&nbsp;||lightpink||1.00||0.75||0.87||<br />
|- align="center"<br />
|bgcolor="#66b2b2"|&nbsp;||lightteal||0.4||0.7||0.7||<br />
|- align="center"<br />
|bgcolor="#7fff7f"|&nbsp;||lime||0.5||1.0||0.5||<br />
|- align="center"<br />
|bgcolor="#00ff7f"|&nbsp;||limegreen||0.0||1.0||0.5||<br />
|- align="center"<br />
|bgcolor="#bfff3f"|&nbsp;||limon||0.75||1.00||0.25||<br />
|- align="center"<br />
|bgcolor="#ff00ff"|&nbsp;||magenta||1.0||0.0||1.0||<br />
|- align="center"<br />
|bgcolor="#007fff"|&nbsp;||marine||0.0||0.5||1.0||<br />
|- align="center"<br />
|bgcolor="#3333ff"|&nbsp;||nitrogen||0.2||0.2||1.0||<br />
|- align="center"<br />
|bgcolor="#c4b200"|&nbsp;||olive||0.77||0.70||0.00||<br />
|- align="center"<br />
|bgcolor="#ff7f00"|&nbsp;||orange||1.0||0.5||0.0||<br />
|- align="center"<br />
|bgcolor="#ff4c4c"|&nbsp;||oxygen||1.0||0.3||0.3||<br />
|- align="center"<br />
|bgcolor="#ccffff"|&nbsp;||palecyan||0.8||1.0||1.0||<br />
|- align="center"<br />
|bgcolor="#a5e5a5"|&nbsp;||palegreen||0.65||0.9||0.65||<br />
|- align="center"<br />
|bgcolor="#ffff7f"|&nbsp;||paleyellow||1.0||1.0||0.5||<br />
|- align="center"<br />
|bgcolor="#ffa5d8"|&nbsp;||pink||1.0||0.65||0.85||<br />
|- align="center"<br />
|bgcolor="#bf00bf"|&nbsp;||purple||0.75||0.00||0.75||<br />
|- align="center"<br />
|bgcolor="#7f00ff"|&nbsp;||purpleblue||0.5||0.0||1.0||legacy name<br />
|- align="center"<br />
|bgcolor="#b24c66"|&nbsp;||raspberry||0.70||0.30||0.40||<br />
|- align="center"<br />
|bgcolor="#ff0000"|&nbsp;||red||1.0||0.0||0.0||<br />
|- align="center"<br />
|bgcolor="#993333"|&nbsp;||ruby||0.6||0.2||0.2||<br />
|- align="center"<br />
|bgcolor="#ff9999"|&nbsp;||salmon||1.0||0.6||0.6||was 0.5<br />
|- align="center"<br />
|bgcolor="#b78c4c"|&nbsp;||sand||0.72||0.55||0.30||<br />
|- align="center"<br />
|bgcolor="#337fcc"|&nbsp;||skyblue||0.20||0.50||0.80||<br />
|- align="center"<br />
|bgcolor="#7f7fff"|&nbsp;||slate||0.5||0.5||1.0||<br />
|- align="center"<br />
|bgcolor="#8cb266"|&nbsp;||smudge||0.55||0.70||0.40||<br />
|- align="center"<br />
|bgcolor="#84bf00"|&nbsp;||splitpea||0.52||0.75||0.00||<br />
|- align="center"<br />
|bgcolor="#e5c53f"|&nbsp;||sulfur||0.9||0.775||0.25||far enough from yellow<br />
|- align="center"<br />
|bgcolor="#00bfbf"|&nbsp;||teal||0.00||0.75||0.75||<br />
|- align="center"<br />
|bgcolor="#4c4cff"|&nbsp;||tv_blue||0.3||0.3||1.0||<br />
|- align="center"<br />
|bgcolor="#33ff33"|&nbsp;||tv_green||0.2||1.0||0.2||<br />
|- align="center"<br />
|bgcolor="#ff8c26"|&nbsp;||tv_orange||1.0||0.55||0.15||<br />
|- align="center"<br />
|bgcolor="#ff3333"|&nbsp;||tv_red||1.0||0.2||0.2||<br />
|- align="center"<br />
|bgcolor="#ffff33"|&nbsp;||tv_yellow||1.0||1.0||0.2||<br />
|- align="center"<br />
|bgcolor="#ff7fff"|&nbsp;||violet||1.0||0.5||1.0||<br />
|- align="center"<br />
|bgcolor="#8c3f99"|&nbsp;||violetpurple||0.55||0.25||0.60||<br />
|- align="center"<br />
|bgcolor="#d8337f"|&nbsp;||warmpink||0.85||0.20||0.50||<br />
|- align="center"<br />
|bgcolor="#fcd1a5"|&nbsp;||wheat||0.99||0.82||0.65||<br />
|- align="center"<br />
|bgcolor="#ffffff"|&nbsp;||white||1.0||1.0||1.0||<br />
|- align="center"<br />
|bgcolor="#ffff00"|&nbsp;||yellow||1.0||1.0||0.0||<br />
|- align="center"<br />
|bgcolor="#ffdd5e"|&nbsp;||yelloworange||1.0||0.87||0.37||<br />
|}<br />
==Chemical element colours==<br />
{| cellpadding="1"<br />
|- align="center"<br />
!width="20"|&nbsp;||bgcolor=gray width="100"|name||bgcolor=red width="50"|R||bgcolor=green width="50"|G||bgcolor=blue width="50"|B||bgcolor=gray|note<br />
|- align="center"<br />
|bgcolor="#6faafa"|&nbsp;||actinium||0.439215686||0.670588235||0.980392157||<br />
|- align="center"<br />
|bgcolor="#bfa5a5"|&nbsp;||aluminum||0.749019608||0.650980392||0.650980392||<br />
|- align="center"<br />
|bgcolor="#545cf2"|&nbsp;||americium||0.329411765||0.360784314||0.949019608||<br />
|- align="center"<br />
|bgcolor="#9d62b5"|&nbsp;||antimony||0.619607843||0.388235294||0.709803922||<br />
|- align="center"<br />
|bgcolor="#7fd0e2"|&nbsp;||argon||0.501960784||0.819607843||0.890196078||<br />
|- align="center"<br />
|bgcolor="#bd7fe2"|&nbsp;||arsenic||0.741176471||0.501960784||0.890196078||<br />
|- align="center"<br />
|bgcolor="#744f44"|&nbsp;||astatine||0.458823529||0.309803922||0.270588235||<br />
|- align="center"<br />
|bgcolor="#00c800"|&nbsp;||barium||0.000000000||0.788235294||0.000000000||<br />
|- align="center"<br />
|bgcolor="#8a4fe2"|&nbsp;||berkelium||0.541176471||0.309803922||0.890196078||<br />
|- align="center"<br />
|bgcolor="#c2ff00"|&nbsp;||beryllium||0.760784314||1.000000000||0.000000000||<br />
|- align="center"<br />
|bgcolor="#9d4fb5"|&nbsp;||bismuth||0.619607843||0.309803922||0.709803922||<br />
|- align="center"<br />
|bgcolor="#e00037"|&nbsp;||bohrium||0.878431373||0.000000000||0.219607843||<br />
|- align="center"<br />
|bgcolor="#ffb5b5"|&nbsp;||boron||1.000000000||0.709803922||0.709803922||<br />
|- align="center"<br />
|bgcolor="#a52929"|&nbsp;||bromine||0.650980392||0.160784314||0.160784314||<br />
|- align="center"<br />
|bgcolor="#ffd88f"|&nbsp;||cadmium||1.000000000||0.850980392||0.560784314||<br />
|- align="center"<br />
|bgcolor="#3cff00"|&nbsp;||calcium||0.239215686||1.000000000||0.000000000||<br />
|- align="center"<br />
|bgcolor="#a036d3"|&nbsp;||californium||0.631372549||0.211764706||0.831372549||<br />
|- align="center"<br />
|bgcolor="#ffffc7"|&nbsp;||cerium||1.000000000||1.000000000||0.780392157||<br />
|- align="center"<br />
|bgcolor="#57168f"|&nbsp;||cesium||0.341176471||0.090196078||0.560784314||<br />
|- align="center"<br />
|bgcolor="#1ef01e"|&nbsp;||chlorine||0.121568627||0.941176471||0.121568627||<br />
|- align="center"<br />
|bgcolor="#8a99c7"|&nbsp;||chromium||0.541176471||0.600000000||0.780392157||<br />
|- align="center"<br />
|bgcolor="#f08f9f"|&nbsp;||cobalt||0.941176471||0.564705882||0.627450980||<br />
|- align="center"<br />
|bgcolor="#c77f33"|&nbsp;||copper||0.784313725||0.501960784||0.200000000||<br />
|- align="center"<br />
|bgcolor="#775ce2"|&nbsp;||curium||0.470588235||0.360784314||0.890196078||<br />
|- align="center"<br />
|bgcolor="#e5e5e5"|&nbsp;||deuterium||0.9||0.9||0.9||<br />
|- align="center"<br />
|bgcolor="#d0004f"|&nbsp;||dubnium||0.819607843||0.000000000||0.309803922||<br />
|- align="center"<br />
|bgcolor="#1effc7"|&nbsp;||dysprosium||0.121568627||1.000000000||0.780392157||<br />
|- align="center"<br />
|bgcolor="#b21ed3"|&nbsp;||einsteinium||0.701960784||0.121568627||0.831372549||<br />
|- align="center"<br />
|bgcolor="#00e574"|&nbsp;||erbium||0.000000000||0.901960784||0.458823529||<br />
|- align="center"<br />
|bgcolor="#61ffc7"|&nbsp;||europium||0.380392157||1.000000000||0.780392157||<br />
|- align="center"<br />
|bgcolor="#b21eba"|&nbsp;||fermium||0.701960784||0.121568627||0.729411765||<br />
|- align="center"<br />
|bgcolor="#b2ffff"|&nbsp;||fluorine||0.701960784||1.000000000||1.000000000||<br />
|- align="center"<br />
|bgcolor="#410066"|&nbsp;||francium||0.258823529||0.000000000||0.400000000||<br />
|- align="center"<br />
|bgcolor="#44ffc7"|&nbsp;||gadolinium||0.270588235||1.000000000||0.780392157||<br />
|- align="center"<br />
|bgcolor="#c28f8f"|&nbsp;||gallium||0.760784314||0.560784314||0.560784314||<br />
|- align="center"<br />
|bgcolor="#668f8f"|&nbsp;||germanium||0.400000000||0.560784314||0.560784314||<br />
|- align="center"<br />
|bgcolor="#ffd023"|&nbsp;||gold||1.000000000||0.819607843||0.137254902||<br />
|- align="center"<br />
|bgcolor="#4cc2ff"|&nbsp;||hafnium||0.301960784||0.760784314||1.000000000||<br />
|- align="center"<br />
|bgcolor="#e5002e"|&nbsp;||hassium||0.901960784||0.000000000||0.180392157||<br />
|- align="center"<br />
|bgcolor="#d8ffff"|&nbsp;||helium||0.850980392||1.000000000||1.000000000||<br />
|- align="center"<br />
|bgcolor="#00ff9c"|&nbsp;||holmium||0.000000000||1.000000000||0.611764706||<br />
|- align="center"<br />
|bgcolor="#a57472"|&nbsp;||indium||0.650980392||0.458823529||0.450980392||<br />
|- align="center"<br />
|bgcolor="#940094"|&nbsp;||iodine||0.580392157||0.000000000||0.580392157||<br />
|- align="center"<br />
|bgcolor="#165487"|&nbsp;||iridium||0.090196078||0.329411765||0.529411765||<br />
|- align="center"<br />
|bgcolor="#e06633"|&nbsp;||iron||0.878431373||0.400000000||0.200000000||<br />
|- align="center"<br />
|bgcolor="#5cb7d0"|&nbsp;||krypton||0.360784314||0.721568627||0.819607843||<br />
|- align="center"<br />
|bgcolor="#6fd3ff"|&nbsp;||lanthanum||0.439215686||0.831372549||1.000000000||<br />
|- align="center"<br />
|bgcolor="#c70066"|&nbsp;||lawrencium||0.780392157||0.000000000||0.400000000||<br />
|- align="center"<br />
|bgcolor="#575961"|&nbsp;||lead||0.341176471||0.349019608||0.380392157||<br />
|- align="center"<br />
|bgcolor="#cc7fff"|&nbsp;||lithium||0.800000000||0.501960784||1.000000000||<br />
|- align="center"<br />
|bgcolor="#00aa24"|&nbsp;||lutetium||0.000000000||0.670588235||0.141176471||<br />
|- align="center"<br />
|bgcolor="#8aff00"|&nbsp;||magnesium||0.541176471||1.000000000||0.000000000||<br />
|- align="center"<br />
|bgcolor="#9c7ac7"|&nbsp;||manganese||0.611764706||0.478431373||0.780392157||<br />
|- align="center"<br />
|bgcolor="#ea0026"|&nbsp;||meitnerium||0.921568627||0.000000000||0.149019608||<br />
|- align="center"<br />
|bgcolor="#b20ca5"|&nbsp;||mendelevium||0.701960784||0.050980392||0.650980392||<br />
|- align="center"<br />
|bgcolor="#b7b7d0"|&nbsp;||mercury||0.721568627||0.721568627||0.815686275||<br />
|- align="center"<br />
|bgcolor="#54b5b5"|&nbsp;||molybdenum||0.329411765||0.709803922||0.709803922||<br />
|- align="center"<br />
|bgcolor="#c7ffc7"|&nbsp;||neodymium||0.780392157||1.000000000||0.780392157||<br />
|- align="center"<br />
|bgcolor="#b2e2f5"|&nbsp;||neon||0.701960784||0.890196078||0.960784314||<br />
|- align="center"<br />
|bgcolor="#007fff"|&nbsp;||neptunium||0.000000000||0.501960784||1.000000000||<br />
|- align="center"<br />
|bgcolor="#4fd04f"|&nbsp;||nickel||0.313725490||0.815686275||0.313725490||<br />
|- align="center"<br />
|bgcolor="#72c2c8"|&nbsp;||niobium||0.450980392||0.760784314||0.788235294||<br />
|- align="center"<br />
|bgcolor="#bd0c87"|&nbsp;||nobelium||0.741176471||0.050980392||0.529411765||<br />
|- align="center"<br />
|bgcolor="#266695"|&nbsp;||osmium||0.149019608||0.400000000||0.588235294||<br />
|- align="center"<br />
|bgcolor="#006984"|&nbsp;||palladium||0.000000000||0.411764706||0.521568627||<br />
|- align="center"<br />
|bgcolor="#ff7f00"|&nbsp;||phosphorus||1.000000000||0.501960784||0.000000000||<br />
|- align="center"<br />
|bgcolor="#d0d0e0"|&nbsp;||platinum||0.815686275||0.815686275||0.878431373||<br />
|- align="center"<br />
|bgcolor="#006aff"|&nbsp;||plutonium||0.000000000||0.419607843||1.000000000||<br />
|- align="center"<br />
|bgcolor="#aa5c00"|&nbsp;||polonium||0.670588235||0.360784314||0.000000000||<br />
|- align="center"<br />
|bgcolor="#8f3fd3"|&nbsp;||potassium||0.560784314||0.250980392||0.831372549||<br />
|- align="center"<br />
|bgcolor="#d8ffc7"|&nbsp;||praseodymium||0.850980392||1.000000000||0.780392157||<br />
|- align="center"<br />
|bgcolor="#a2ffc7"|&nbsp;||promethium||0.639215686||1.000000000||0.780392157||<br />
|- align="center"<br />
|bgcolor="#00a0ff"|&nbsp;||protactinium||0.000000000||0.631372549||1.000000000||<br />
|- align="center"<br />
|bgcolor="#007c00"|&nbsp;||radium||0.000000000||0.490196078||0.000000000||<br />
|- align="center"<br />
|bgcolor="#418295"|&nbsp;||radon||0.258823529||0.509803922||0.588235294||<br />
|- align="center"<br />
|bgcolor="#267caa"|&nbsp;||rhenium||0.149019608||0.490196078||0.670588235||<br />
|- align="center"<br />
|bgcolor="#097c8c"|&nbsp;||rhodium||0.039215686||0.490196078||0.549019608||<br />
|- align="center"<br />
|bgcolor="#6f2eaf"|&nbsp;||rubidium||0.439215686||0.180392157||0.690196078||<br />
|- align="center"<br />
|bgcolor="#248f8f"|&nbsp;||ruthenium||0.141176471||0.560784314||0.560784314||<br />
|- align="center"<br />
|bgcolor="#cc0059"|&nbsp;||rutherfordium||0.800000000||0.000000000||0.349019608||<br />
|- align="center"<br />
|bgcolor="#8fffc7"|&nbsp;||samarium||0.560784314||1.000000000||0.780392157||<br />
|- align="center"<br />
|bgcolor="#e5e5e5"|&nbsp;||scandium||0.901960784||0.901960784||0.901960784||<br />
|- align="center"<br />
|bgcolor="#d80044"|&nbsp;||seaborgium||0.850980392||0.000000000||0.270588235||<br />
|- align="center"<br />
|bgcolor="#ffa000"|&nbsp;||selenium||1.000000000||0.631372549||0.000000000||<br />
|- align="center"<br />
|bgcolor="#f0c79f"|&nbsp;||silicon||0.941176471||0.784313725||0.627450980||<br />
|- align="center"<br />
|bgcolor="#bfbfbf"|&nbsp;||silver||0.752941176||0.752941176||0.752941176||<br />
|- align="center"<br />
|bgcolor="#aa5cf2"|&nbsp;||sodium||0.670588235||0.360784314||0.949019608||<br />
|- align="center"<br />
|bgcolor="#00ff00"|&nbsp;||strontium||0.000000000||1.000000000||0.000000000||<br />
|- align="center"<br />
|bgcolor="#4ca5ff"|&nbsp;||tantalum||0.301960784||0.650980392||1.000000000||<br />
|- align="center"<br />
|bgcolor="#3a9d9d"|&nbsp;||technetium||0.231372549||0.619607843||0.619607843||<br />
|- align="center"<br />
|bgcolor="#d37a00"|&nbsp;||tellurium||0.831372549||0.478431373||0.000000000||<br />
|- align="center"<br />
|bgcolor="#2fffc7"|&nbsp;||terbium||0.188235294||1.000000000||0.780392157||<br />
|- align="center"<br />
|bgcolor="#a5544c"|&nbsp;||thallium||0.650980392||0.329411765||0.301960784||<br />
|- align="center"<br />
|bgcolor="#00baff"|&nbsp;||thorium||0.000000000||0.729411765||1.000000000||<br />
|- align="center"<br />
|bgcolor="#00d351"|&nbsp;||thulium||0.000000000||0.831372549||0.321568627||<br />
|- align="center"<br />
|bgcolor="#667f7f"|&nbsp;||tin||0.400000000||0.501960784||0.501960784||<br />
|- align="center"<br />
|bgcolor="#bfc2c7"|&nbsp;||titanium||0.749019608||0.760784314||0.780392157||<br />
|- align="center"<br />
|bgcolor="#2194d5"|&nbsp;||tungsten||0.129411765||0.580392157||0.839215686||<br />
|- align="center"<br />
|bgcolor="#008fff"|&nbsp;||uranium||0.000000000||0.560784314||1.000000000||<br />
|- align="center"<br />
|bgcolor="#a5a5aa"|&nbsp;||vanadium||0.650980392||0.650980392||0.670588235||<br />
|- align="center"<br />
|bgcolor="#419daf"|&nbsp;||xenon||0.258823529||0.619607843||0.690196078||<br />
|- align="center"<br />
|bgcolor="#00bf37"|&nbsp;||ytterbium||0.000000000||0.749019608||0.219607843||<br />
|- align="center"<br />
|bgcolor="#94ffff"|&nbsp;||yttrium||0.580392157||1.000000000||1.000000000||<br />
|- align="center"<br />
|bgcolor="#7c7faf"|&nbsp;||zinc||0.490196078||0.501960784||0.690196078||<br />
|- align="center"<br />
|bgcolor="#94e0e0"|&nbsp;||zirconium||0.580392157||0.878431373||0.878431373||<br />
|}<br />
==Interactive menu colours==<br />
Accessible from Colour submenu of objects<br />
===reds===<br />
{| cellpadding="1" <br />
|- align="center" <br />
!width="20"|&nbsp;||bgcolor=gray width="100"|name||bgcolor=red width="50"|R||bgcolor=green width="50"|G||bgcolor=blue width="50"|B||<br />
|- align="center" <br />
|bgcolor="#ff0000"|&nbsp;||red||1.0||0.0||0.0||<br />
|- align="center" <br />
|bgcolor="#ff3333"|&nbsp;||tv_red||1.0||0.2||0.2||<br />
|- align="center" <br />
|bgcolor="#b24c66"|&nbsp;||raspberry||0.70||0.30||0.40||<br />
|- align="center" <br />
|bgcolor="#ba8c84"|&nbsp;||darksalmon||0.73||0.55||0.52||<br />
|- align="center" <br />
|bgcolor="#ff9999"|&nbsp;||salmon||1.0||0.6||0.6||<br />
|- align="center" <br />
|bgcolor="#ff6b6b"|&nbsp;||deepsalmon||1.00||0.42||0.42||<br />
|- align="center" <br />
|bgcolor="#d8337f"|&nbsp;||warmpink||0.85||0.20||0.50||<br />
|- align="center" <br />
|bgcolor="#b12121"|&nbsp;||firebrick||0.698||0.13||0.13||<br />
|- align="center" <br />
|bgcolor="#993333"|&nbsp;||ruby||0.6||0.2||0.2||<br />
|- align="center" <br />
|bgcolor="#8d381c"|&nbsp;||chocolate||0.555||0.222||0.111||<br />
|- align="center" <br />
|bgcolor="#a5512b"|&nbsp;||brown||0.65||0.32||0.17||<br />
|}<br />
===greens===<br />
{| cellpadding="1" <br />
|- align="center" <br />
!width="20"|&nbsp;||bgcolor=gray width="100"|name||bgcolor=red width="50"|R||bgcolor=green width="50"|G||bgcolor=blue width="50"|B||<br />
|- align="center" <br />
|bgcolor="#00ff00"|&nbsp;||green||0.0||1.0||0.0||<br />
|- align="center" <br />
|bgcolor="#33ff33"|&nbsp;||tv_green||0.2||1.0||0.2||<br />
|- align="center" <br />
|bgcolor="#7fff00"|&nbsp;||chartreuse||0.5||1.0||0.0||<br />
|- align="center" <br />
|bgcolor="#84bf00"|&nbsp;||splitpea||0.52||0.75||0.00||<br />
|- align="center" <br />
|bgcolor="#8cb266"|&nbsp;||smudge||0.55||0.70||0.40||<br />
|- align="center" <br />
|bgcolor="#a5e5a5"|&nbsp;||palegreen||0.65||0.9||0.65||<br />
|- align="center" <br />
|bgcolor="#00ff7f"|&nbsp;||limegreen||0.0||1.0||0.5||<br />
|- align="center" <br />
|bgcolor="#7fff7f"|&nbsp;||lime||0.5||1.0||0.5||<br />
|- align="center" <br />
|bgcolor="#bfff3f"|&nbsp;||limon||0.75||1.00||0.25||<br />
|- align="center" <br />
|bgcolor="#339933"|&nbsp;||forest||0.2||0.6||0.2||<br />
|}<br />
===blues===<br />
{| cellpadding="1" <br />
|- align="center" <br />
!width="20"|&nbsp;||bgcolor=gray width="100"|name||bgcolor=red width="50"|R||bgcolor=green width="50"|G||bgcolor=blue width="50"|B||<br />
|- align="center" <br />
|bgcolor="#0000ff"|&nbsp;||blue||0.0||0.0||1.0||<br />
|- align="center" <br />
|bgcolor="#4c4cff"|&nbsp;||tv_blue||0.3||0.3||1.0||<br />
|- align="center" <br />
|bgcolor="#007fff"|&nbsp;||marine||0.0||0.5||1.0||<br />
|- align="center" <br />
|bgcolor="#7f7fff"|&nbsp;||slate||0.5||0.5||1.0||<br />
|- align="center" <br />
|bgcolor="#bfbfff"|&nbsp;||lightblue||0.75||0.75||1.0||<br />
|- align="center" <br />
|bgcolor="#337fcc"|&nbsp;||skyblue||0.20||0.50||0.80||<br />
|- align="center" <br />
|bgcolor="#7f00ff"|&nbsp;||purpleblue||0.5||0.0||1.0||<br />
|- align="center" <br />
|bgcolor="#3f3fa5"|&nbsp;||deepblue||0.25||0.25||0.65||<br />
|- align="center" <br />
|bgcolor="#191999"|&nbsp;||density||0.1||0.1||0.6||<br />
|}<br />
===yellows===<br />
{| cellpadding="1" <br />
|- align="center" <br />
!width="20"|&nbsp;||bgcolor=gray width="100"|name||bgcolor=red width="50"|R||bgcolor=green width="50"|G||bgcolor=blue width="50"|B||<br />
|- align="center" <br />
|bgcolor="#ffff00"|&nbsp;||yellow||1.0||1.0||0.0||<br />
|- align="center" <br />
|bgcolor="#ffff33"|&nbsp;||tv_yellow||1.0||1.0||0.2||<br />
|- align="center" <br />
|bgcolor="#ffff7f"|&nbsp;||paleyellow||1.0||1.0||0.5||<br />
|- align="center" <br />
|bgcolor="#ffdd5e"|&nbsp;||yelloworange||1.0||0.87||0.37||<br />
|- align="center" <br />
|bgcolor="#bfff3f"|&nbsp;||limon||0.75||1.00||0.25||<br />
|- align="center" <br />
|bgcolor="#fcd1a5"|&nbsp;||wheat||0.99||0.82||0.65||<br />
|- align="center" <br />
|bgcolor="#b78c4c"|&nbsp;||sand||0.72||0.55||0.30||<br />
|}<br />
===magentas===<br />
{| cellpadding="1" <br />
|- align="center" <br />
!width="20"|&nbsp;||bgcolor=gray width="100"|name||bgcolor=red width="50"|R||bgcolor=green width="50"|G||bgcolor=blue width="50"|B||<br />
|- align="center" <br />
|bgcolor="#ff00ff"|&nbsp;||magenta||1.0||0.0||1.0||<br />
|- align="center" <br />
|bgcolor="#ff33cc"|&nbsp;||lightmagenta||1.0||0.2||0.8||<br />
|- align="center" <br />
|bgcolor="#ff007f"|&nbsp;||hotpink||1.0||0.0||0.5||<br />
|- align="center" <br />
|bgcolor="#ffa5d8"|&nbsp;||pink||1.0||0.65||0.85||<br />
|- align="center" <br />
|bgcolor="#ffbfdd"|&nbsp;||lightpink||1.00||0.75||0.87||<br />
|- align="center" <br />
|bgcolor="#b27f7f"|&nbsp;||dirtyviolet||0.70||0.50||0.50||<br />
|- align="center" <br />
|bgcolor="#ff7fff"|&nbsp;||violet||1.0||0.5||1.0||<br />
|- align="center" <br />
|bgcolor="#8c3f99"|&nbsp;||violetpurple||0.55||0.25||0.60||<br />
|- align="center" <br />
|bgcolor="#bf00bf"|&nbsp;||purple||0.75||0.00||0.75||<br />
|- align="center" <br />
|bgcolor="#991999"|&nbsp;||deeppurple||0.6||0.1||0.6||<br />
|}<br />
===cyans===<br />
{| cellpadding="1" <br />
|- align="center" <br />
!width="20"|&nbsp;||bgcolor=gray width="100"|name||bgcolor=red width="50"|R||bgcolor=green width="50"|G||bgcolor=blue width="50"|B||<br />
|- align="center" <br />
|bgcolor="#00ffff"|&nbsp;||cyan||0.0||1.0||1.0||<br />
|- align="center" <br />
|bgcolor="#ccffff"|&nbsp;||palecyan||0.8||1.0||1.0||<br />
|- align="center" <br />
|bgcolor="#7fffff"|&nbsp;||aquamarine||0.5||1.0||1.0||<br />
|- align="center" <br />
|bgcolor="#3fffbf"|&nbsp;||greencyan||0.25||1.00||0.75||<br />
|- align="center" <br />
|bgcolor="#00bfbf"|&nbsp;||teal||0.00||0.75||0.75||<br />
|- align="center" <br />
|bgcolor="#199999"|&nbsp;||deepteal||0.1||0.6||0.6||<br />
|- align="center" <br />
|bgcolor="#66b2b2"|&nbsp;||lightteal||0.4||0.7||0.7||<br />
|}<br />
===oranges===<br />
{| cellpadding="1" <br />
|- align="center" <br />
!width="20"|&nbsp;||bgcolor=gray width="100"|name||bgcolor=red width="50"|R||bgcolor=green width="50"|G||bgcolor=blue width="50"|B||<br />
|- align="center" <br />
|bgcolor="#ff7f00"|&nbsp;||orange||1.0||0.5||0.0||<br />
|- align="center" <br />
|bgcolor="#ff8c26"|&nbsp;||tv_orange||1.0||0.55||0.15||<br />
|- align="center" <br />
|bgcolor="#ffb233"|&nbsp;||brightorange||1.0||0.7||0.2||<br />
|- align="center" <br />
|bgcolor="#ffcc7f"|&nbsp;||lightorange||1.0||0.8||0.5||<br />
|- align="center" <br />
|bgcolor="#ffdd5e"|&nbsp;||yelloworange||1.0||0.87||0.37||<br />
|- align="center" <br />
|bgcolor="#c4b200"|&nbsp;||olive||0.77||0.70||0.00||<br />
|- align="center" <br />
|bgcolor="#999919"|&nbsp;||deepolive||0.6||0.6||0.1||<br />
|}<br />
===tints===<br />
{| cellpadding="1" <br />
|- align="center" <br />
!width="20"|&nbsp;||bgcolor=gray width="100"|name||bgcolor=red width="50"|R||bgcolor=green width="50"|G||bgcolor=blue width="50"|B||<br />
|- align="center" <br />
|bgcolor="#fcd1a5"|&nbsp;||wheat||0.99||0.82||0.65||<br />
|- align="center" <br />
|bgcolor="#a5e5a5"|&nbsp;||palegreen||0.65||0.9||0.65||<br />
|- align="center" <br />
|bgcolor="#bfbfff"|&nbsp;||lightblue||0.75||0.75||1.0||<br />
|- align="center" <br />
|bgcolor="#ffff7f"|&nbsp;||paleyellow||1.0||1.0||0.5||<br />
|- align="center" <br />
|bgcolor="#ffbfdd"|&nbsp;||lightpink||1.00||0.75||0.87||<br />
|- align="center" <br />
|bgcolor="#ccffff"|&nbsp;||palecyan||0.8||1.0||1.0||<br />
|- align="center" <br />
|bgcolor="#ffcc7f"|&nbsp;||lightorange||1.0||0.8||0.5||<br />
|- align="center" <br />
|bgcolor="#d8d8ff"|&nbsp;||bluewhite||0.85||0.85||1.00||<br />
|}<br />
===grays===<br />
{| cellpadding="1" <br />
|- align="center" <br />
!width="20"|&nbsp;||bgcolor=gray width="100"|name||bgcolor=red width="50"|R||bgcolor=green width="50"|G||bgcolor=blue width="50"|B||<br />
|- align="center" <br />
|bgcolor="#ffffff"|&nbsp;||white||1.0||1.0||1.0||<br />
|- align="center" <br />
|bgcolor="#e5e5e5"|&nbsp;||grey90||0.9||0.9||0.9||<br />
|- align="center" <br />
|bgcolor="#cccccc"|&nbsp;||grey80||0.8||0.8||0.8||<br />
|- align="center" <br />
|bgcolor="#b2b2b2"|&nbsp;||grey70||0.7||0.7||0.7||<br />
|- align="center" <br />
|bgcolor="#999999"|&nbsp;||grey60||0.6||0.6||0.6||<br />
|- align="center" <br />
|bgcolor="#7f7f7f"|&nbsp;||grey50||0.5||0.5||0.5||<br />
|- align="center" <br />
|bgcolor="#666666"|&nbsp;||grey40||0.4||0.4||0.4||<br />
|- align="center" <br />
|bgcolor="#4c4c4c"|&nbsp;||grey30||0.3||0.3||0.3||<br />
|- align="center" <br />
|bgcolor="#333333"|&nbsp;||grey20||0.2||0.2||0.2||<br />
|- align="center" <br />
|bgcolor="#191919"|&nbsp;||grey10||0.1||0.1||0.1||<br />
|- align="center" <br />
|bgcolor="#000000"|&nbsp;||black||0.0||0.0||0.0||<br />
|}<br />
==Secondary structure colour schemes==<br />
Accessible from 'by ss' section within Colour submenu of object<br />
{| cellpadding="1" <br />
|- align="center" <br />
!bgcolor=gray width="100" colspan="1"|helix||bgcolor=gray width="100" colspan="1"|sheet||bgcolor=gray width="100" colspan="1"|loop<br />
|- align="center" <br />
|bgcolor="#ff0000"|red||bgcolor="#ffff00"|yellow||bgcolor="#00ff00"|green<br />
|- align="center" <br />
|bgcolor="#00ffff"|cyan||bgcolor="#ff00ff"|magenta||bgcolor="#ff9999"|salmon<br />
|}<br />
==Carbon colour schemes==<br />
*Accessible from 'by element' section within Colour submenu of object<br />
*Only carbon colour is affected, other elements are set to their default element colour<br />
*Separated into five sets:<br />
**main set<br />
{| cellpadding="1" <br />
|- align="left" <br />
!width="20"|&nbsp;||bgcolor=gray|name<br />
|- align="left" <br />
|&nbsp;||(carbon not changed)<br />
|- align="left" <br />
|bgcolor="#33ff33"|&nbsp;||carbon<br />
|- align="left" <br />
|bgcolor="#00ffff"|&nbsp;||cyan<br />
|- align="left" <br />
|bgcolor="#ff33cc"|&nbsp;||lightmagenta<br />
|- align="left" <br />
|bgcolor="#ffff00"|&nbsp;||yellow<br />
|- align="left" <br />
|bgcolor="#ff9999"|&nbsp;||salmon<br />
|- align="left" <br />
|bgcolor="#e5e5e5"|&nbsp;||hydrogen<br />
|- align="left" <br />
|bgcolor="#7f7fff"|&nbsp;||slate<br />
|- align="left" <br />
|bgcolor="#ff7f00"|&nbsp;||orange<br />
|}<br />
**set2<br />
{| cellpadding="1" <br />
|- align="left" <br />
!width="20"|&nbsp;||bgcolor=gray|name<br />
|- align="left" <br />
|bgcolor="#7fff7f"|&nbsp;||lime<br />
|- align="left" <br />
|bgcolor="#199999"|&nbsp;||deepteal<br />
|- align="left" <br />
|bgcolor="#ff007f"|&nbsp;||hotpink<br />
|- align="left" <br />
|bgcolor="#ffdd5e"|&nbsp;||yelloworange<br />
|- align="left" <br />
|bgcolor="#8c3f99"|&nbsp;||violetpurple<br />
|- align="left" <br />
|bgcolor="#b2b2b2"|&nbsp;||grey70<br />
|- align="left" <br />
|bgcolor="#007fff"|&nbsp;||marine<br />
|- align="left" <br />
|bgcolor="#c4b200"|&nbsp;||olive<br />
|}<br />
**set3<br />
{| cellpadding="1" <br />
|- align="left" <br />
!width="20"|&nbsp;||bgcolor=gray|name<br />
|- align="left" <br />
|bgcolor="#8cb266"|&nbsp;||smudge<br />
|- align="left" <br />
|bgcolor="#00bfbf"|&nbsp;||teal<br />
|- align="left" <br />
|bgcolor="#b27f7f"|&nbsp;||dirtyviolet<br />
|- align="left" <br />
|bgcolor="#fcd1a5"|&nbsp;||wheat<br />
|- align="left" <br />
|bgcolor="#ff7f7f"|&nbsp;||deepsalmon<br />
|- align="left" <br />
|bgcolor="#ffbfdd"|&nbsp;||lightpink<br />
|- align="left" <br />
|bgcolor="#7fffff"|&nbsp;||aquamarine<br />
|- align="left" <br />
|bgcolor="#ffff7f"|&nbsp;||paleyellow<br />
|}<br />
**set4<br />
{| cellpadding="1" <br />
|- align="left" <br />
!width="20"|&nbsp;||bgcolor=gray|name<br />
|- align="left" <br />
|bgcolor="#00ff7f"|&nbsp;||limegreen<br />
|- align="left" <br />
|bgcolor="#337fcc"|&nbsp;||skyblue<br />
|- align="left" <br />
|bgcolor="#d8337f"|&nbsp;||warmpink<br />
|- align="left" <br />
|bgcolor="#bfff3f"|&nbsp;||limon<br />
|- align="left" <br />
|bgcolor="#ff7fff"|&nbsp;||violet<br />
|- align="left" <br />
|bgcolor="#d8d8ff"|&nbsp;||bluewhite<br />
|- align="left" <br />
|bgcolor="#3fffbf"|&nbsp;||greencyan<br />
|- align="left" <br />
|bgcolor="#b78c4c"|&nbsp;||sand<br />
|}<br />
**set 5<br />
{| cellpadding="1"<br />
|- align="left" <br />
!width="20"|&nbsp;||bgcolor=gray|name<br />
|- align="left" <br />
|bgcolor="#339933"|&nbsp;||forest<br />
|- align="left" <br />
|bgcolor="#66b2b2"|&nbsp;||lightteal<br />
|- align="left" <br />
|bgcolor="#ba8c84"|&nbsp;||darksalmon<br />
|- align="left" <br />
|bgcolor="#84bf00"|&nbsp;||splitpea<br />
|- align="left" <br />
|bgcolor="#b24c66"|&nbsp;||raspberry<br />
|- align="left" <br />
|bgcolor="#7f7f7f"|&nbsp;||grey50<br />
|- align="left" <br />
|bgcolor="#3f3fa5"|&nbsp;||deepblue<br />
|- align="left" <br />
|bgcolor="#a5512b"|&nbsp;||brown<br />
|}</div>Aflaushttps://pymolwiki.org/index.php?title=Color_Values&diff=1143Color Values2005-11-18T01:36:44Z<p>Aflaus: </p>
<hr />
<div>==Background==<br />
*Naming<br />
**All listed colours can be specified by name<br />
**American and English spellings of gray/grey and color/colour can be used<br />
*Sources<br />
**Pymol colours are specified as triples of proportion of Red, Green and Blue<br />
**Colour specs from source files Color.c, menu.py and appearance.py of Pymol 0.99 beta29<br />
==Spectral range colours==<br />
Spectral ranges are available by name including a numerical value (eg grey56, s532)<br />
*Grays from gray00 to gray99 (white to black)<br />
*Spectrum from s000 to s999 (violet to red)<br />
*Original spectrum with extra blue and red at ends from o000 to o999<br />
*Reversed offset spectrum from r000 to r999<br />
*Complementary spectrum from c000 to c999<br />
*Complementary spectrum separated by white from w000 to w999<br />
See Colour.c in source code for details about how spectra are calculated<br />
==Simple named colours==<br />
{| cellpadding="1"<br />
|- align="center"<br />
!width="20"|&nbsp;||bgcolor=gray width="100"|name||bgcolor=red width="50"|R||bgcolor=green width="50"|G||bgcolor=blue width="50"|B||bgcolor=gray|note<br />
|- align="center"<br />
|bgcolor="#7fffff"|&nbsp;||aquamarine||0.5||1.0||1.0||<br />
|- align="center"<br />
|bgcolor="#000000"|&nbsp;||black||0.0||0.0||0.0||<br />
|- align="center"<br />
|bgcolor="#0000ff"|&nbsp;||blue||0.0||0.0||1.0||<br />
|- align="center"<br />
|bgcolor="#d8d8ff"|&nbsp;||bluewhite||0.85||0.85||1.00||<br />
|- align="center"<br />
|bgcolor="#1919ff"|&nbsp;||br0||0.1||0.1||1.0||<br />
|- align="center"<br />
|bgcolor="#3319e5"|&nbsp;||br1||0.2||0.1||0.9||<br />
|- align="center"<br />
|bgcolor="#4c19cc"|&nbsp;||br2||0.3||0.1||0.8||<br />
|- align="center"<br />
|bgcolor="#6619b2"|&nbsp;||br3||0.4||0.1||0.7||<br />
|- align="center"<br />
|bgcolor="#7f1999"|&nbsp;||br4||0.5||0.1||0.6||<br />
|- align="center"<br />
|bgcolor="#99197f"|&nbsp;||br5||0.6||0.1||0.5||<br />
|- align="center"<br />
|bgcolor="#b21966"|&nbsp;||br6||0.7||0.1||0.4||<br />
|- align="center"<br />
|bgcolor="#cc194c"|&nbsp;||br7||0.8||0.1||0.3||<br />
|- align="center"<br />
|bgcolor="#e51933"|&nbsp;||br8||0.9||0.1||0.2||<br />
|- align="center"<br />
|bgcolor="#ff1919"|&nbsp;||br9||1.0||0.1||0.1||<br />
|- align="center"<br />
|bgcolor="#ffb233"|&nbsp;||brightorange||1.0||0.7||0.2||<br />
|- align="center"<br />
|bgcolor="#a5512b"|&nbsp;||brown||0.65||0.32||0.17||<br />
|- align="center"<br />
|bgcolor="#33ff33"|&nbsp;||carbon||0.2||1.0||0.2||<br />
|- align="center"<br />
|bgcolor="#7fff00"|&nbsp;||chartreuse||0.5||1.0||0.0||AKA puke green<br />
|- align="center"<br />
|bgcolor="#8d381c"|&nbsp;||chocolate||0.555||0.222||0.111||<br />
|- align="center"<br />
|bgcolor="#00ffff"|&nbsp;||cyan||0.0||1.0||1.0||<br />
|- align="center"<br />
|bgcolor="#ba8c84"|&nbsp;||darksalmon||0.73||0.55||0.52||<br />
|- align="center"<br />
|bgcolor="#ffff00"|&nbsp;||dash||1.0||1.0||0.0||<br />
|- align="center"<br />
|bgcolor="#3f3fa5"|&nbsp;||deepblue||0.25||0.25||0.65||deep<br />
|- align="center"<br />
|bgcolor="#999919"|&nbsp;||deepolive||0.6||0.6||0.1||<br />
|- align="center"<br />
|bgcolor="#991999"|&nbsp;||deeppurple||0.6||0.1||0.6||<br />
|- align="center"<br />
|bgcolor="#ff7f7f"|&nbsp;||deepsalmon||1.0||0.5||0.5||duplicated?<br />
|- align="center"<br />
|bgcolor="#ff6b6b"|&nbsp;||deepsalmon||1.00||0.42||0.42||duplicated?<br />
|- align="center"<br />
|bgcolor="#199999"|&nbsp;||deepteal||0.1||0.6||0.6||<br />
|- align="center"<br />
|bgcolor="#191999"|&nbsp;||density||0.1||0.1||0.6||<br />
|- align="center"<br />
|bgcolor="#b27f7f"|&nbsp;||dirtyviolet||0.70||0.50||0.50||<br />
|- align="center"<br />
|bgcolor="#b12121"|&nbsp;||firebrick||0.698||0.13||0.13||<br />
|- align="center"<br />
|bgcolor="#339933"|&nbsp;||forest||0.2||0.6||0.2||<br />
|- align="center"<br />
|bgcolor="#7f7f7f"|&nbsp;||gray||0.5||0.5||0.5||american spelling<br />
|- align="center"<br />
|bgcolor="#00ff00"|&nbsp;||green||0.0||1.0||0.0||<br />
|- align="center"<br />
|bgcolor="#3fffbf"|&nbsp;||greencyan||0.25||1.00||0.75||<br />
|- align="center"<br />
|bgcolor="#7f7f7f"|&nbsp;||grey||0.5||0.5||0.5||english spelling<br />
|- align="center"<br />
|bgcolor="#ff007f"|&nbsp;||hotpink||1.0||0.0||0.5||<br />
|- align="center"<br />
|bgcolor="#e5e5e5"|&nbsp;||hydrogen||0.9||0.9||0.9||<br />
|- align="center"<br />
|bgcolor="#bfbfff"|&nbsp;||lightblue||0.75||0.75||1.0||<br />
|- align="center"<br />
|bgcolor="#ff33cc"|&nbsp;||lightmagenta||1.0||0.2||0.8||<br />
|- align="center"<br />
|bgcolor="#ffcc7f"|&nbsp;||lightorange||1.0||0.8||0.5||<br />
|- align="center"<br />
|bgcolor="#ffbfdd"|&nbsp;||lightpink||1.00||0.75||0.87||<br />
|- align="center"<br />
|bgcolor="#66b2b2"|&nbsp;||lightteal||0.4||0.7||0.7||<br />
|- align="center"<br />
|bgcolor="#7fff7f"|&nbsp;||lime||0.5||1.0||0.5||<br />
|- align="center"<br />
|bgcolor="#00ff7f"|&nbsp;||limegreen||0.0||1.0||0.5||<br />
|- align="center"<br />
|bgcolor="#bfff3f"|&nbsp;||limon||0.75||1.00||0.25||<br />
|- align="center"<br />
|bgcolor="#ff00ff"|&nbsp;||magenta||1.0||0.0||1.0||<br />
|- align="center"<br />
|bgcolor="#007fff"|&nbsp;||marine||0.0||0.5||1.0||<br />
|- align="center"<br />
|bgcolor="#3333ff"|&nbsp;||nitrogen||0.2||0.2||1.0||<br />
|- align="center"<br />
|bgcolor="#c4b200"|&nbsp;||olive||0.77||0.70||0.00||<br />
|- align="center"<br />
|bgcolor="#ff7f00"|&nbsp;||orange||1.0||0.5||0.0||<br />
|- align="center"<br />
|bgcolor="#ff4c4c"|&nbsp;||oxygen||1.0||0.3||0.3||<br />
|- align="center"<br />
|bgcolor="#ccffff"|&nbsp;||palecyan||0.8||1.0||1.0||<br />
|- align="center"<br />
|bgcolor="#a5e5a5"|&nbsp;||palegreen||0.65||0.9||0.65||<br />
|- align="center"<br />
|bgcolor="#ffff7f"|&nbsp;||paleyellow||1.0||1.0||0.5||<br />
|- align="center"<br />
|bgcolor="#ffa5d8"|&nbsp;||pink||1.0||0.65||0.85||<br />
|- align="center"<br />
|bgcolor="#bf00bf"|&nbsp;||purple||0.75||0.00||0.75||<br />
|- align="center"<br />
|bgcolor="#7f00ff"|&nbsp;||purpleblue||0.5||0.0||1.0||legacy name<br />
|- align="center"<br />
|bgcolor="#b24c66"|&nbsp;||raspberry||0.70||0.30||0.40||<br />
|- align="center"<br />
|bgcolor="#ff0000"|&nbsp;||red||1.0||0.0||0.0||<br />
|- align="center"<br />
|bgcolor="#993333"|&nbsp;||ruby||0.6||0.2||0.2||<br />
|- align="center"<br />
|bgcolor="#ff9999"|&nbsp;||salmon||1.0||0.6||0.6||was 0.5<br />
|- align="center"<br />
|bgcolor="#b78c4c"|&nbsp;||sand||0.72||0.55||0.30||<br />
|- align="center"<br />
|bgcolor="#337fcc"|&nbsp;||skyblue||0.20||0.50||0.80||<br />
|- align="center"<br />
|bgcolor="#7f7fff"|&nbsp;||slate||0.5||0.5||1.0||<br />
|- align="center"<br />
|bgcolor="#8cb266"|&nbsp;||smudge||0.55||0.70||0.40||<br />
|- align="center"<br />
|bgcolor="#84bf00"|&nbsp;||splitpea||0.52||0.75||0.00||<br />
|- align="center"<br />
|bgcolor="#e5c53f"|&nbsp;||sulfur||0.9||0.775||0.25||far enough from yellow<br />
|- align="center"<br />
|bgcolor="#00bfbf"|&nbsp;||teal||0.00||0.75||0.75||<br />
|- align="center"<br />
|bgcolor="#4c4cff"|&nbsp;||tv_blue||0.3||0.3||1.0||<br />
|- align="center"<br />
|bgcolor="#33ff33"|&nbsp;||tv_green||0.2||1.0||0.2||<br />
|- align="center"<br />
|bgcolor="#ff8c26"|&nbsp;||tv_orange||1.0||0.55||0.15||<br />
|- align="center"<br />
|bgcolor="#ff3333"|&nbsp;||tv_red||1.0||0.2||0.2||<br />
|- align="center"<br />
|bgcolor="#ffff33"|&nbsp;||tv_yellow||1.0||1.0||0.2||<br />
|- align="center"<br />
|bgcolor="#ff7fff"|&nbsp;||violet||1.0||0.5||1.0||<br />
|- align="center"<br />
|bgcolor="#8c3f99"|&nbsp;||violetpurple||0.55||0.25||0.60||<br />
|- align="center"<br />
|bgcolor="#d8337f"|&nbsp;||warmpink||0.85||0.20||0.50||<br />
|- align="center"<br />
|bgcolor="#fcd1a5"|&nbsp;||wheat||0.99||0.82||0.65||<br />
|- align="center"<br />
|bgcolor="#ffffff"|&nbsp;||white||1.0||1.0||1.0||<br />
|- align="center"<br />
|bgcolor="#ffff00"|&nbsp;||yellow||1.0||1.0||0.0||<br />
|- align="center"<br />
|bgcolor="#ffdd5e"|&nbsp;||yelloworange||1.0||0.87||0.37||<br />
|}<br />
==Chemical element colours==<br />
{| cellpadding="1"<br />
|- align="center"<br />
!width="20"|&nbsp;||bgcolor=gray width="100"|name||bgcolor=red width="50"|R||bgcolor=green width="50"|G||bgcolor=blue width="50"|B||bgcolor=gray|note<br />
|- align="center"<br />
|bgcolor="#6faafa"|&nbsp;||actinium||0.439215686||0.670588235||0.980392157||<br />
|- align="center"<br />
|bgcolor="#bfa5a5"|&nbsp;||aluminum||0.749019608||0.650980392||0.650980392||<br />
|- align="center"<br />
|bgcolor="#545cf2"|&nbsp;||americium||0.329411765||0.360784314||0.949019608||<br />
|- align="center"<br />
|bgcolor="#9d62b5"|&nbsp;||antimony||0.619607843||0.388235294||0.709803922||<br />
|- align="center"<br />
|bgcolor="#7fd0e2"|&nbsp;||argon||0.501960784||0.819607843||0.890196078||<br />
|- align="center"<br />
|bgcolor="#bd7fe2"|&nbsp;||arsenic||0.741176471||0.501960784||0.890196078||<br />
|- align="center"<br />
|bgcolor="#744f44"|&nbsp;||astatine||0.458823529||0.309803922||0.270588235||<br />
|- align="center"<br />
|bgcolor="#00c800"|&nbsp;||barium||0.000000000||0.788235294||0.000000000||<br />
|- align="center"<br />
|bgcolor="#8a4fe2"|&nbsp;||berkelium||0.541176471||0.309803922||0.890196078||<br />
|- align="center"<br />
|bgcolor="#c2ff00"|&nbsp;||beryllium||0.760784314||1.000000000||0.000000000||<br />
|- align="center"<br />
|bgcolor="#9d4fb5"|&nbsp;||bismuth||0.619607843||0.309803922||0.709803922||<br />
|- align="center"<br />
|bgcolor="#e00037"|&nbsp;||bohrium||0.878431373||0.000000000||0.219607843||<br />
|- align="center"<br />
|bgcolor="#ffb5b5"|&nbsp;||boron||1.000000000||0.709803922||0.709803922||<br />
|- align="center"<br />
|bgcolor="#a52929"|&nbsp;||bromine||0.650980392||0.160784314||0.160784314||<br />
|- align="center"<br />
|bgcolor="#ffd88f"|&nbsp;||cadmium||1.000000000||0.850980392||0.560784314||<br />
|- align="center"<br />
|bgcolor="#3cff00"|&nbsp;||calcium||0.239215686||1.000000000||0.000000000||<br />
|- align="center"<br />
|bgcolor="#a036d3"|&nbsp;||californium||0.631372549||0.211764706||0.831372549||<br />
|- align="center"<br />
|bgcolor="#ffffc7"|&nbsp;||cerium||1.000000000||1.000000000||0.780392157||<br />
|- align="center"<br />
|bgcolor="#57168f"|&nbsp;||cesium||0.341176471||0.090196078||0.560784314||<br />
|- align="center"<br />
|bgcolor="#1ef01e"|&nbsp;||chlorine||0.121568627||0.941176471||0.121568627||<br />
|- align="center"<br />
|bgcolor="#8a99c7"|&nbsp;||chromium||0.541176471||0.600000000||0.780392157||<br />
|- align="center"<br />
|bgcolor="#f08f9f"|&nbsp;||cobalt||0.941176471||0.564705882||0.627450980||<br />
|- align="center"<br />
|bgcolor="#c77f33"|&nbsp;||copper||0.784313725||0.501960784||0.200000000||<br />
|- align="center"<br />
|bgcolor="#775ce2"|&nbsp;||curium||0.470588235||0.360784314||0.890196078||<br />
|- align="center"<br />
|bgcolor="#e5e5e5"|&nbsp;||deuterium||0.9||0.9||0.9||<br />
|- align="center"<br />
|bgcolor="#d0004f"|&nbsp;||dubnium||0.819607843||0.000000000||0.309803922||<br />
|- align="center"<br />
|bgcolor="#1effc7"|&nbsp;||dysprosium||0.121568627||1.000000000||0.780392157||<br />
|- align="center"<br />
|bgcolor="#b21ed3"|&nbsp;||einsteinium||0.701960784||0.121568627||0.831372549||<br />
|- align="center"<br />
|bgcolor="#00e574"|&nbsp;||erbium||0.000000000||0.901960784||0.458823529||<br />
|- align="center"<br />
|bgcolor="#61ffc7"|&nbsp;||europium||0.380392157||1.000000000||0.780392157||<br />
|- align="center"<br />
|bgcolor="#b21eba"|&nbsp;||fermium||0.701960784||0.121568627||0.729411765||<br />
|- align="center"<br />
|bgcolor="#b2ffff"|&nbsp;||fluorine||0.701960784||1.000000000||1.000000000||<br />
|- align="center"<br />
|bgcolor="#410066"|&nbsp;||francium||0.258823529||0.000000000||0.400000000||<br />
|- align="center"<br />
|bgcolor="#44ffc7"|&nbsp;||gadolinium||0.270588235||1.000000000||0.780392157||<br />
|- align="center"<br />
|bgcolor="#c28f8f"|&nbsp;||gallium||0.760784314||0.560784314||0.560784314||<br />
|- align="center"<br />
|bgcolor="#668f8f"|&nbsp;||germanium||0.400000000||0.560784314||0.560784314||<br />
|- align="center"<br />
|bgcolor="#ffd023"|&nbsp;||gold||1.000000000||0.819607843||0.137254902||<br />
|- align="center"<br />
|bgcolor="#4cc2ff"|&nbsp;||hafnium||0.301960784||0.760784314||1.000000000||<br />
|- align="center"<br />
|bgcolor="#e5002e"|&nbsp;||hassium||0.901960784||0.000000000||0.180392157||<br />
|- align="center"<br />
|bgcolor="#d8ffff"|&nbsp;||helium||0.850980392||1.000000000||1.000000000||<br />
|- align="center"<br />
|bgcolor="#00ff9c"|&nbsp;||holmium||0.000000000||1.000000000||0.611764706||<br />
|- align="center"<br />
|bgcolor="#a57472"|&nbsp;||indium||0.650980392||0.458823529||0.450980392||<br />
|- align="center"<br />
|bgcolor="#940094"|&nbsp;||iodine||0.580392157||0.000000000||0.580392157||<br />
|- align="center"<br />
|bgcolor="#165487"|&nbsp;||iridium||0.090196078||0.329411765||0.529411765||<br />
|- align="center"<br />
|bgcolor="#e06633"|&nbsp;||iron||0.878431373||0.400000000||0.200000000||<br />
|- align="center"<br />
|bgcolor="#5cb7d0"|&nbsp;||krypton||0.360784314||0.721568627||0.819607843||<br />
|- align="center"<br />
|bgcolor="#6fd3ff"|&nbsp;||lanthanum||0.439215686||0.831372549||1.000000000||<br />
|- align="center"<br />
|bgcolor="#c70066"|&nbsp;||lawrencium||0.780392157||0.000000000||0.400000000||<br />
|- align="center"<br />
|bgcolor="#575961"|&nbsp;||lead||0.341176471||0.349019608||0.380392157||<br />
|- align="center"<br />
|bgcolor="#cc7fff"|&nbsp;||lithium||0.800000000||0.501960784||1.000000000||<br />
|- align="center"<br />
|bgcolor="#00aa24"|&nbsp;||lutetium||0.000000000||0.670588235||0.141176471||<br />
|- align="center"<br />
|bgcolor="#8aff00"|&nbsp;||magnesium||0.541176471||1.000000000||0.000000000||<br />
|- align="center"<br />
|bgcolor="#9c7ac7"|&nbsp;||manganese||0.611764706||0.478431373||0.780392157||<br />
|- align="center"<br />
|bgcolor="#ea0026"|&nbsp;||meitnerium||0.921568627||0.000000000||0.149019608||<br />
|- align="center"<br />
|bgcolor="#b20ca5"|&nbsp;||mendelevium||0.701960784||0.050980392||0.650980392||<br />
|- align="center"<br />
|bgcolor="#b7b7d0"|&nbsp;||mercury||0.721568627||0.721568627||0.815686275||<br />
|- align="center"<br />
|bgcolor="#54b5b5"|&nbsp;||molybdenum||0.329411765||0.709803922||0.709803922||<br />
|- align="center"<br />
|bgcolor="#c7ffc7"|&nbsp;||neodymium||0.780392157||1.000000000||0.780392157||<br />
|- align="center"<br />
|bgcolor="#b2e2f5"|&nbsp;||neon||0.701960784||0.890196078||0.960784314||<br />
|- align="center"<br />
|bgcolor="#007fff"|&nbsp;||neptunium||0.000000000||0.501960784||1.000000000||<br />
|- align="center"<br />
|bgcolor="#4fd04f"|&nbsp;||nickel||0.313725490||0.815686275||0.313725490||<br />
|- align="center"<br />
|bgcolor="#72c2c8"|&nbsp;||niobium||0.450980392||0.760784314||0.788235294||<br />
|- align="center"<br />
|bgcolor="#bd0c87"|&nbsp;||nobelium||0.741176471||0.050980392||0.529411765||<br />
|- align="center"<br />
|bgcolor="#266695"|&nbsp;||osmium||0.149019608||0.400000000||0.588235294||<br />
|- align="center"<br />
|bgcolor="#006984"|&nbsp;||palladium||0.000000000||0.411764706||0.521568627||<br />
|- align="center"<br />
|bgcolor="#ff7f00"|&nbsp;||phosphorus||1.000000000||0.501960784||0.000000000||<br />
|- align="center"<br />
|bgcolor="#d0d0e0"|&nbsp;||platinum||0.815686275||0.815686275||0.878431373||<br />
|- align="center"<br />
|bgcolor="#006aff"|&nbsp;||plutonium||0.000000000||0.419607843||1.000000000||<br />
|- align="center"<br />
|bgcolor="#aa5c00"|&nbsp;||polonium||0.670588235||0.360784314||0.000000000||<br />
|- align="center"<br />
|bgcolor="#8f3fd3"|&nbsp;||potassium||0.560784314||0.250980392||0.831372549||<br />
|- align="center"<br />
|bgcolor="#d8ffc7"|&nbsp;||praseodymium||0.850980392||1.000000000||0.780392157||<br />
|- align="center"<br />
|bgcolor="#a2ffc7"|&nbsp;||promethium||0.639215686||1.000000000||0.780392157||<br />
|- align="center"<br />
|bgcolor="#00a0ff"|&nbsp;||protactinium||0.000000000||0.631372549||1.000000000||<br />
|- align="center"<br />
|bgcolor="#007c00"|&nbsp;||radium||0.000000000||0.490196078||0.000000000||<br />
|- align="center"<br />
|bgcolor="#418295"|&nbsp;||radon||0.258823529||0.509803922||0.588235294||<br />
|- align="center"<br />
|bgcolor="#267caa"|&nbsp;||rhenium||0.149019608||0.490196078||0.670588235||<br />
|- align="center"<br />
|bgcolor="#097c8c"|&nbsp;||rhodium||0.039215686||0.490196078||0.549019608||<br />
|- align="center"<br />
|bgcolor="#6f2eaf"|&nbsp;||rubidium||0.439215686||0.180392157||0.690196078||<br />
|- align="center"<br />
|bgcolor="#248f8f"|&nbsp;||ruthenium||0.141176471||0.560784314||0.560784314||<br />
|- align="center"<br />
|bgcolor="#cc0059"|&nbsp;||rutherfordium||0.800000000||0.000000000||0.349019608||<br />
|- align="center"<br />
|bgcolor="#8fffc7"|&nbsp;||samarium||0.560784314||1.000000000||0.780392157||<br />
|- align="center"<br />
|bgcolor="#e5e5e5"|&nbsp;||scandium||0.901960784||0.901960784||0.901960784||<br />
|- align="center"<br />
|bgcolor="#d80044"|&nbsp;||seaborgium||0.850980392||0.000000000||0.270588235||<br />
|- align="center"<br />
|bgcolor="#ffa000"|&nbsp;||selenium||1.000000000||0.631372549||0.000000000||<br />
|- align="center"<br />
|bgcolor="#f0c79f"|&nbsp;||silicon||0.941176471||0.784313725||0.627450980||<br />
|- align="center"<br />
|bgcolor="#bfbfbf"|&nbsp;||silver||0.752941176||0.752941176||0.752941176||<br />
|- align="center"<br />
|bgcolor="#aa5cf2"|&nbsp;||sodium||0.670588235||0.360784314||0.949019608||<br />
|- align="center"<br />
|bgcolor="#00ff00"|&nbsp;||strontium||0.000000000||1.000000000||0.000000000||<br />
|- align="center"<br />
|bgcolor="#4ca5ff"|&nbsp;||tantalum||0.301960784||0.650980392||1.000000000||<br />
|- align="center"<br />
|bgcolor="#3a9d9d"|&nbsp;||technetium||0.231372549||0.619607843||0.619607843||<br />
|- align="center"<br />
|bgcolor="#d37a00"|&nbsp;||tellurium||0.831372549||0.478431373||0.000000000||<br />
|- align="center"<br />
|bgcolor="#2fffc7"|&nbsp;||terbium||0.188235294||1.000000000||0.780392157||<br />
|- align="center"<br />
|bgcolor="#a5544c"|&nbsp;||thallium||0.650980392||0.329411765||0.301960784||<br />
|- align="center"<br />
|bgcolor="#00baff"|&nbsp;||thorium||0.000000000||0.729411765||1.000000000||<br />
|- align="center"<br />
|bgcolor="#00d351"|&nbsp;||thulium||0.000000000||0.831372549||0.321568627||<br />
|- align="center"<br />
|bgcolor="#667f7f"|&nbsp;||tin||0.400000000||0.501960784||0.501960784||<br />
|- align="center"<br />
|bgcolor="#bfc2c7"|&nbsp;||titanium||0.749019608||0.760784314||0.780392157||<br />
|- align="center"<br />
|bgcolor="#2194d5"|&nbsp;||tungsten||0.129411765||0.580392157||0.839215686||<br />
|- align="center"<br />
|bgcolor="#008fff"|&nbsp;||uranium||0.000000000||0.560784314||1.000000000||<br />
|- align="center"<br />
|bgcolor="#a5a5aa"|&nbsp;||vanadium||0.650980392||0.650980392||0.670588235||<br />
|- align="center"<br />
|bgcolor="#419daf"|&nbsp;||xenon||0.258823529||0.619607843||0.690196078||<br />
|- align="center"<br />
|bgcolor="#00bf37"|&nbsp;||ytterbium||0.000000000||0.749019608||0.219607843||<br />
|- align="center"<br />
|bgcolor="#94ffff"|&nbsp;||yttrium||0.580392157||1.000000000||1.000000000||<br />
|- align="center"<br />
|bgcolor="#7c7faf"|&nbsp;||zinc||0.490196078||0.501960784||0.690196078||<br />
|- align="center"<br />
|bgcolor="#94e0e0"|&nbsp;||zirconium||0.580392157||0.878431373||0.878431373||<br />
|}<br />
==Interactive menu colours==<br />
from menu.py<br />
===reds===<br />
{| cellpadding="1" <br />
|- align="center" <br />
!width="20"|&nbsp;||bgcolor=gray width="100"|name||bgcolor=red width="50"|R||bgcolor=green width="50"|G||bgcolor=blue width="50"|B||<br />
|- align="center" <br />
|bgcolor="#ff0000"|&nbsp;||red||1.0||0.0||0.0||<br />
|- align="center" <br />
|bgcolor="#ff3333"|&nbsp;||tv_red||1.0||0.2||0.2||<br />
|- align="center" <br />
|bgcolor="#b24c66"|&nbsp;||raspberry||0.70||0.30||0.40||<br />
|- align="center" <br />
|bgcolor="#ba8c84"|&nbsp;||darksalmon||0.73||0.55||0.52||<br />
|- align="center" <br />
|bgcolor="#ff9999"|&nbsp;||salmon||1.0||0.6||0.6||<br />
|- align="center" <br />
|bgcolor="#ff6b6b"|&nbsp;||deepsalmon||1.00||0.42||0.42||<br />
|- align="center" <br />
|bgcolor="#d8337f"|&nbsp;||warmpink||0.85||0.20||0.50||<br />
|- align="center" <br />
|bgcolor="#b12121"|&nbsp;||firebrick||0.698||0.13||0.13||<br />
|- align="center" <br />
|bgcolor="#993333"|&nbsp;||ruby||0.6||0.2||0.2||<br />
|- align="center" <br />
|bgcolor="#8d381c"|&nbsp;||chocolate||0.555||0.222||0.111||<br />
|- align="center" <br />
|bgcolor="#a5512b"|&nbsp;||brown||0.65||0.32||0.17||<br />
|}<br />
===greens===<br />
{| cellpadding="1" <br />
|- align="center" <br />
!width="20"|&nbsp;||bgcolor=gray width="100"|name||bgcolor=red width="50"|R||bgcolor=green width="50"|G||bgcolor=blue width="50"|B||<br />
|- align="center" <br />
|bgcolor="#00ff00"|&nbsp;||green||0.0||1.0||0.0||<br />
|- align="center" <br />
|bgcolor="#33ff33"|&nbsp;||tv_green||0.2||1.0||0.2||<br />
|- align="center" <br />
|bgcolor="#7fff00"|&nbsp;||chartreuse||0.5||1.0||0.0||<br />
|- align="center" <br />
|bgcolor="#84bf00"|&nbsp;||splitpea||0.52||0.75||0.00||<br />
|- align="center" <br />
|bgcolor="#8cb266"|&nbsp;||smudge||0.55||0.70||0.40||<br />
|- align="center" <br />
|bgcolor="#a5e5a5"|&nbsp;||palegreen||0.65||0.9||0.65||<br />
|- align="center" <br />
|bgcolor="#00ff7f"|&nbsp;||limegreen||0.0||1.0||0.5||<br />
|- align="center" <br />
|bgcolor="#7fff7f"|&nbsp;||lime||0.5||1.0||0.5||<br />
|- align="center" <br />
|bgcolor="#bfff3f"|&nbsp;||limon||0.75||1.00||0.25||<br />
|- align="center" <br />
|bgcolor="#339933"|&nbsp;||forest||0.2||0.6||0.2||<br />
|}<br />
===blues===<br />
{| cellpadding="1" <br />
|- align="center" <br />
!width="20"|&nbsp;||bgcolor=gray width="100"|name||bgcolor=red width="50"|R||bgcolor=green width="50"|G||bgcolor=blue width="50"|B||<br />
|- align="center" <br />
|bgcolor="#0000ff"|&nbsp;||blue||0.0||0.0||1.0||<br />
|- align="center" <br />
|bgcolor="#4c4cff"|&nbsp;||tv_blue||0.3||0.3||1.0||<br />
|- align="center" <br />
|bgcolor="#007fff"|&nbsp;||marine||0.0||0.5||1.0||<br />
|- align="center" <br />
|bgcolor="#7f7fff"|&nbsp;||slate||0.5||0.5||1.0||<br />
|- align="center" <br />
|bgcolor="#bfbfff"|&nbsp;||lightblue||0.75||0.75||1.0||<br />
|- align="center" <br />
|bgcolor="#337fcc"|&nbsp;||skyblue||0.20||0.50||0.80||<br />
|- align="center" <br />
|bgcolor="#7f00ff"|&nbsp;||purpleblue||0.5||0.0||1.0||<br />
|- align="center" <br />
|bgcolor="#3f3fa5"|&nbsp;||deepblue||0.25||0.25||0.65||<br />
|- align="center" <br />
|bgcolor="#191999"|&nbsp;||density||0.1||0.1||0.6||<br />
|}<br />
===yellows===<br />
{| cellpadding="1" <br />
|- align="center" <br />
!width="20"|&nbsp;||bgcolor=gray width="100"|name||bgcolor=red width="50"|R||bgcolor=green width="50"|G||bgcolor=blue width="50"|B||<br />
|- align="center" <br />
|bgcolor="#ffff00"|&nbsp;||yellow||1.0||1.0||0.0||<br />
|- align="center" <br />
|bgcolor="#ffff33"|&nbsp;||tv_yellow||1.0||1.0||0.2||<br />
|- align="center" <br />
|bgcolor="#ffff7f"|&nbsp;||paleyellow||1.0||1.0||0.5||<br />
|- align="center" <br />
|bgcolor="#ffdd5e"|&nbsp;||yelloworange||1.0||0.87||0.37||<br />
|- align="center" <br />
|bgcolor="#bfff3f"|&nbsp;||limon||0.75||1.00||0.25||<br />
|- align="center" <br />
|bgcolor="#fcd1a5"|&nbsp;||wheat||0.99||0.82||0.65||<br />
|- align="center" <br />
|bgcolor="#b78c4c"|&nbsp;||sand||0.72||0.55||0.30||<br />
|}<br />
===magentas===<br />
{| cellpadding="1" <br />
|- align="center" <br />
!width="20"|&nbsp;||bgcolor=gray width="100"|name||bgcolor=red width="50"|R||bgcolor=green width="50"|G||bgcolor=blue width="50"|B||<br />
|- align="center" <br />
|bgcolor="#ff00ff"|&nbsp;||magenta||1.0||0.0||1.0||<br />
|- align="center" <br />
|bgcolor="#ff33cc"|&nbsp;||lightmagenta||1.0||0.2||0.8||<br />
|- align="center" <br />
|bgcolor="#ff007f"|&nbsp;||hotpink||1.0||0.0||0.5||<br />
|- align="center" <br />
|bgcolor="#ffa5d8"|&nbsp;||pink||1.0||0.65||0.85||<br />
|- align="center" <br />
|bgcolor="#ffbfdd"|&nbsp;||lightpink||1.00||0.75||0.87||<br />
|- align="center" <br />
|bgcolor="#b27f7f"|&nbsp;||dirtyviolet||0.70||0.50||0.50||<br />
|- align="center" <br />
|bgcolor="#ff7fff"|&nbsp;||violet||1.0||0.5||1.0||<br />
|- align="center" <br />
|bgcolor="#8c3f99"|&nbsp;||violetpurple||0.55||0.25||0.60||<br />
|- align="center" <br />
|bgcolor="#bf00bf"|&nbsp;||purple||0.75||0.00||0.75||<br />
|- align="center" <br />
|bgcolor="#991999"|&nbsp;||deeppurple||0.6||0.1||0.6||<br />
|}<br />
===cyans===<br />
{| cellpadding="1" <br />
|- align="center" <br />
!width="20"|&nbsp;||bgcolor=gray width="100"|name||bgcolor=red width="50"|R||bgcolor=green width="50"|G||bgcolor=blue width="50"|B||<br />
|- align="center" <br />
|bgcolor="#00ffff"|&nbsp;||cyan||0.0||1.0||1.0||<br />
|- align="center" <br />
|bgcolor="#ccffff"|&nbsp;||palecyan||0.8||1.0||1.0||<br />
|- align="center" <br />
|bgcolor="#7fffff"|&nbsp;||aquamarine||0.5||1.0||1.0||<br />
|- align="center" <br />
|bgcolor="#3fffbf"|&nbsp;||greencyan||0.25||1.00||0.75||<br />
|- align="center" <br />
|bgcolor="#00bfbf"|&nbsp;||teal||0.00||0.75||0.75||<br />
|- align="center" <br />
|bgcolor="#199999"|&nbsp;||deepteal||0.1||0.6||0.6||<br />
|- align="center" <br />
|bgcolor="#66b2b2"|&nbsp;||lightteal||0.4||0.7||0.7||<br />
|}<br />
===oranges===<br />
{| cellpadding="1" <br />
|- align="center" <br />
!width="20"|&nbsp;||bgcolor=gray width="100"|name||bgcolor=red width="50"|R||bgcolor=green width="50"|G||bgcolor=blue width="50"|B||<br />
|- align="center" <br />
|bgcolor="#ff7f00"|&nbsp;||orange||1.0||0.5||0.0||<br />
|- align="center" <br />
|bgcolor="#ff8c26"|&nbsp;||tv_orange||1.0||0.55||0.15||<br />
|- align="center" <br />
|bgcolor="#ffb233"|&nbsp;||brightorange||1.0||0.7||0.2||<br />
|- align="center" <br />
|bgcolor="#ffcc7f"|&nbsp;||lightorange||1.0||0.8||0.5||<br />
|- align="center" <br />
|bgcolor="#ffdd5e"|&nbsp;||yelloworange||1.0||0.87||0.37||<br />
|- align="center" <br />
|bgcolor="#c4b200"|&nbsp;||olive||0.77||0.70||0.00||<br />
|- align="center" <br />
|bgcolor="#999919"|&nbsp;||deepolive||0.6||0.6||0.1||<br />
|}<br />
===tints===<br />
{| cellpadding="1" <br />
|- align="center" <br />
!width="20"|&nbsp;||bgcolor=gray width="100"|name||bgcolor=red width="50"|R||bgcolor=green width="50"|G||bgcolor=blue width="50"|B||<br />
|- align="center" <br />
|bgcolor="#fcd1a5"|&nbsp;||wheat||0.99||0.82||0.65||<br />
|- align="center" <br />
|bgcolor="#a5e5a5"|&nbsp;||palegreen||0.65||0.9||0.65||<br />
|- align="center" <br />
|bgcolor="#bfbfff"|&nbsp;||lightblue||0.75||0.75||1.0||<br />
|- align="center" <br />
|bgcolor="#ffff7f"|&nbsp;||paleyellow||1.0||1.0||0.5||<br />
|- align="center" <br />
|bgcolor="#ffbfdd"|&nbsp;||lightpink||1.00||0.75||0.87||<br />
|- align="center" <br />
|bgcolor="#ccffff"|&nbsp;||palecyan||0.8||1.0||1.0||<br />
|- align="center" <br />
|bgcolor="#ffcc7f"|&nbsp;||lightorange||1.0||0.8||0.5||<br />
|- align="center" <br />
|bgcolor="#d8d8ff"|&nbsp;||bluewhite||0.85||0.85||1.00||<br />
|}<br />
===grays===<br />
{| cellpadding="1" <br />
|- align="center" <br />
!width="20"|&nbsp;||bgcolor=gray width="100"|name||bgcolor=red width="50"|R||bgcolor=green width="50"|G||bgcolor=blue width="50"|B||<br />
|- align="center" <br />
|bgcolor="#ffffff"|&nbsp;||white||1.0||1.0||1.0||<br />
|- align="center" <br />
|bgcolor="#e5e5e5"|&nbsp;||grey90||0.9||0.9||0.9||<br />
|- align="center" <br />
|bgcolor="#cccccc"|&nbsp;||grey80||0.8||0.8||0.8||<br />
|- align="center" <br />
|bgcolor="#b2b2b2"|&nbsp;||grey70||0.7||0.7||0.7||<br />
|- align="center" <br />
|bgcolor="#999999"|&nbsp;||grey60||0.6||0.6||0.6||<br />
|- align="center" <br />
|bgcolor="#7f7f7f"|&nbsp;||grey50||0.5||0.5||0.5||<br />
|- align="center" <br />
|bgcolor="#666666"|&nbsp;||grey40||0.4||0.4||0.4||<br />
|- align="center" <br />
|bgcolor="#4c4c4c"|&nbsp;||grey30||0.3||0.3||0.3||<br />
|- align="center" <br />
|bgcolor="#333333"|&nbsp;||grey20||0.2||0.2||0.2||<br />
|- align="center" <br />
|bgcolor="#191919"|&nbsp;||grey10||0.1||0.1||0.1||<br />
|- align="center" <br />
|bgcolor="#000000"|&nbsp;||black||0.0||0.0||0.0||<br />
|}<br />
==Secondary structure colour schemes==<br />
from menu.py<br />
{| cellpadding="1" <br />
|- align="center" <br />
!bgcolor=gray width="100" colspan="1"|helix||bgcolor=gray width="100" colspan="1"|sheet||bgcolor=gray width="100" colspan="1"|loop<br />
|- align="center" <br />
|bgcolor="#ff0000"|red||bgcolor="#ffff00"|yellow||bgcolor="#00ff00"|green<br />
|- align="center" <br />
|bgcolor="#00ffff"|cyan||bgcolor="#ff00ff"|magenta||bgcolor="#ff9999"|salmon<br />
|}<br />
==Molecule element colour schemes==<br />
Listed below are the colours displayed in the menu for the C,H,N,O,S atoms and what appears to be the default colour for other atoms. For more exact details, see menu.py in source code.<br />
===set1===<br />
{| cellpadding="1" <br />
|- align="center" <br />
!bgcolor=gray colspan="3"|C||bgcolor=gray colspan="3"|H||bgcolor=gray colspan="3"|N||bgcolor=gray colspan="3"|O||bgcolor=gray colspan="3"|S||bgcolor=gray colspan="3"|other<br />
|- align="center" <br />
!width="40"|R||width="40"|G||width="40"|B||width="40"|R||width="40"|G||width="40"|B||width="40"|R||width="40"|G||width="40"|B||width="40"|R||width="40"|G||width="40"|B||width="40"|R||width="40"|G||width="40"|B||code||name<br />
|- align="center" <br />
|0||0||0||7||7||7||2||2||9||9||2||2||9||5||0||||atomic<br />
|- align="center" <br />
|2||9||2||7||7||7||2||2||9||9||2||2||9||5||0||26||carbon<br />
|- align="center" <br />
|0||9||9||7||7||7||2||2||9||9||2||2||9||5||0||5||cyan<br />
|- align="center" <br />
|9||2||7||7||7||7||2||2||9||9||2||2||9||5||0||154||lightmagenta<br />
|- align="center" <br />
|9||9||0||7||7||7||2||2||9||9||2||2||9||5||0||6||yellow<br />
|- align="center" <br />
|9||5||5||7||7||7||2||2||9||9||2||2||9||5||0||9||salmon<br />
|- align="center" <br />
|8||8||8||7||7||7||2||2||9||9||2||2||9||5||0||29||hydrogen<br />
|- align="center" <br />
|4||4||9||7||7||7||2||2||9||9||2||2||9||5||0||11||slate<br />
|- align="center" <br />
|9||6||2||7||7||7||2||2||9||9||2||2||9||5||0||13||orange<br />
|}<br />
===set2===<br />
{| cellpadding="1" <br />
|- align="center" <br />
!bgcolor=gray colspan="3"|C||bgcolor=gray colspan="3"|H||bgcolor=gray colspan="3"|N||bgcolor=gray colspan="3"|O||bgcolor=gray colspan="3"|S||bgcolor=gray colspan="3"|other<br />
|- align="center" <br />
!width="40"|R||width="40"|G||width="40"|B||width="40"|R||width="40"|G||width="40"|B||width="40"|R||width="40"|G||width="40"|B||width="40"|R||width="40"|G||width="40"|B||width="40"|R||width="40"|G||width="40"|B||code||name<br />
|- align="center" <br />
|4||9||4||7||7||7||2||2||9||9||2||2||9||5||0||10||lime<br />
|- align="center" <br />
|1||5||5||7||7||7||2||2||9||9||2||2||9||5||0||5262||deepteal<br />
|- align="center" <br />
|9||0||4||7||7||7||2||2||9||9||2||2||9||5||0||12||hotpink<br />
|- align="center" <br />
|9||8||3||7||7||7||2||2||9||9||2||2||9||5||0||36||yelloworange<br />
|- align="center" <br />
|5||2||5||7||7||7||2||2||9||9||2||2||9||5||0||5271||violetpurple<br />
|- align="center" <br />
|6||6||6||7||7||7||2||2||9||9||2||2||9||5||0||124||grey70<br />
|- align="center" <br />
|0||4||9||7||7||7||2||2||9||9||2||2||9||5||0||17||marine<br />
|- align="center" <br />
|7||6||0||7||7||7||2||2||9||9||2||2||9||5||0||18||olive<br />
|}<br />
===set3===<br />
{| cellpadding="1" <br />
|- align="center" <br />
!bgcolor=gray colspan="3"|C||bgcolor=gray colspan="3"|H||bgcolor=gray colspan="3"|N||bgcolor=gray colspan="3"|O||bgcolor=gray colspan="3"|S||bgcolor=gray colspan="3"|other<br />
|- align="center" <br />
!width="40"|R||width="40"|G||width="40"|B||width="40"|R||width="40"|G||width="40"|B||width="40"|R||width="40"|G||width="40"|B||width="40"|R||width="40"|G||width="40"|B||width="40"|R||width="40"|G||width="40"|B||code||name<br />
|- align="center" <br />
|5||6||4||7||7||7||2||2||9||9||2||2||9||5||0||5270||smudge<br />
|- align="center" <br />
|0||7||7||7||7||7||2||2||9||9||2||2||9||5||0||20||teal<br />
|- align="center" <br />
|6||4||4||7||7||7||2||2||9||9||2||2||9||5||0||5272||dirtyviolet<br />
|- align="center" <br />
|9||7||6||7||7||7||2||2||9||9||2||2||9||5||0||52||wheat<br />
|- align="center" <br />
|9||4||4||7||7||7||2||2||9||9||2||2||9||5||0||5258||deepsalmon<br />
|- align="center" <br />
|9||7||8||7||7||7||2||2||9||9||2||2||9||5||0||5274||lightpink<br />
|- align="center" <br />
|4||9||9||7||7||7||2||2||9||9||2||2||9||5||0||5257||aquamarine<br />
|- align="center" <br />
|9||9||4||7||7||7||2||2||9||9||2||2||9||5||0||5256||paleyellow<br />
|}<br />
===set4===<br />
{| cellpadding="1" <br />
|- align="center" <br />
!bgcolor=gray colspan="3"|C||bgcolor=gray colspan="3"|H||bgcolor=gray colspan="3"|N||bgcolor=gray colspan="3"|O||bgcolor=gray colspan="3"|S||bgcolor=gray colspan="3"|other<br />
|- align="center" <br />
!width="40"|R||width="40"|G||width="40"|B||width="40"|R||width="40"|G||width="40"|B||width="40"|R||width="40"|G||width="40"|B||width="40"|R||width="40"|G||width="40"|B||width="40"|R||width="40"|G||width="40"|B||code||name<br />
|- align="center" <br />
|0||9||4||7||7||7||2||2||9||9||2||2||9||5||0||15||limegreen<br />
|- align="center" <br />
|2||4||7||7||7||7||2||2||9||9||2||2||9||5||0||5277||skyblue<br />
|- align="center" <br />
|8||2||4||7||7||7||2||2||9||9||2||2||9||5||0||5279||warmpink<br />
|- align="center" <br />
|7||9||2||7||7||7||2||2||9||9||2||2||9||5||0||5276||limon<br />
|- align="center" <br />
|9||4||9||7||7||7||2||2||9||9||2||2||9||5||0||53||violet<br />
|- align="center" <br />
|8||8||9||7||7||7||2||2||9||9||2||2||9||5||0||5278||bluewhite<br />
|- align="center" <br />
|2||9||7||7||7||7||2||2||9||9||2||2||9||5||0||5275||greencyan<br />
|- align="center" <br />
|6||5||3||7||7||7||2||2||9||9||2||2||9||5||0||5269||sand<br />
|}<br />
===set5===<br />
{| cellpadding="1"<br />
|- align="center" <br />
!bgcolor=gray colspan="3"|C||bgcolor=gray colspan="3"|H||bgcolor=gray colspan="3"|N||bgcolor=gray colspan="3"|O||bgcolor=gray colspan="3"|S||bgcolor=gray colspan="3"|other<br />
|- align="center" <br />
!width="40"|R||width="40"|G||width="40"|B||width="40"|R||width="40"|G||width="40"|B||width="40"|R||width="40"|G||width="40"|B||width="40"|R||width="40"|G||width="40"|B||width="40"|R||width="40"|G||width="40"|B||code||name<br />
|- align="center" <br />
|2||5||2||7||7||7||2||2||9||9||2||2||9||5||0||22||forest<br />
|- align="center" <br />
|4||6||6||7||7||7||2||2||9||9||2||2||9||5||0||5266||lightteal<br />
|- align="center" <br />
|7||5||5||7||7||7||2||2||9||9||2||2||9||5||0||5280||darksalmon<br />
|- align="center" <br />
|5||7||0||7||7||7||2||2||9||9||2||2||9||5||0||5267||splitpea<br />
|- align="center" <br />
|6||3||4||7||7||7||2||2||9||9||2||2||9||5||0||5268||raspberry<br />
|- align="center" <br />
|5||5||5||7||7||7||2||2||9||9||2||2||9||5||0||104||grey50<br />
|- align="center" <br />
|2||2||6||7||7||7||2||2||9||9||2||2||9||5||0||23||deepblue<br />
|- align="center" <br />
|6||3||2||7||7||7||2||2||9||9||2||2||9||5||0||51||brown<br />
|}</div>Aflaushttps://pymolwiki.org/index.php?title=Color&diff=3146Color2005-11-17T19:26:02Z<p>Aflaus: </p>
<hr />
<div>===DESCRIPTION===<br />
'''color''' changes the color of an object or an atom selection.<br />
<br />
===USAGE===<br />
color color-name<br />
color color-name, object-name<br />
color color-name, (selection)<br />
<br />
===PYMOL API===<br />
<source lang="python">cmd.color( string color, string selection )</source><br />
<br />
==Using RGB for Color==<br />
If you prefer RGB to color any object<br />
<source lang="python"><br />
set_color newcolor, [r,g,b]<br />
color newcolor<br />
</source><br />
List of [[Color Values]]<br />
<br />
===EXAMPLES===<br />
<source lang="python">color yellow, (name C*)</source><br />
<br />
RGB Example:<br />
<source lang="python"><br />
set_color khaki, [195,176,145]<br />
color khaki<br />
</source><br />
<br />
[[Category:Objects_and_Selections]]<br />
[[Category:Commands|color]]</div>Aflaushttps://pymolwiki.org/index.php?title=Examples_of_nucleic_acid_cartoons&diff=3299Examples of nucleic acid cartoons2005-11-10T20:42:12Z<p>Aflaus: Examples of cartoon_ring and cartoon_ladder modes</p>
<hr />
<div>== pymol version info ==<br />
The various new nucleic acid display settings for PyMol 0.99 listed below were produced using version 0.99 beta 29 on Windows XP with an arbitrary B-form DNA molecule. Higher values could be set for each setting but appeared to yield the default representations.<br />
== default settings ==<br />
The defaults give a phosphate backbone with single sticks passing across the full width of the base plane.<br />
<source lang="python"><br />
set cartoon_nucleic_acid_mode, 1 # backbone follows phosphates<br />
set cartoon_ladder_mode, 1 # sticks from backbone into nucleotide<br />
set cartoon_ring_mode, 0 # no nucleotide rings<br />
set cartoon_ring_finder, 1 # ribose and base rings (not displayed as ring mode 0)<br />
</source><br />
{|<br />
|[[Image:DNAcartoon_ringmode0_laddermode1_ringfinder1_nucleicacidmode0.png|default view|thumb]]<br />
|}<br />
== cartoon ring modes ==<br />
<source lang="python"><br />
set cartoon_ring_mode, 0 # no nucleotide rings<br />
set cartoon_ring_mode, 1 # filled rings extending to outside edge of bonds<br />
set cartoon_ring_mode, 2 # filled rings extending to inside edge of bonds<br />
set cartoon_ring_mode, 3 # filled rings with bonds as thicker lines<br />
</source><br />
{|<br />
|[[Image:DNAcartoon_ringmode0_laddermode1_ringfinder1_nucleicacidmode0.png|cartoon_ring_mode,0|thumb]]<br />
|[[Image:DNAcartoon_ringmode1_laddermode1_ringfinder1_nucleicacidmode0.png|cartoon_ring_mode,1|thumb]]<br />
|[[Image:DNAcartoon_ringmode2_laddermode1_ringfinder1_nucleicacidmode0.png|cartoon_ring_mode,2|thumb]]<br />
|[[Image:DNAcartoon_ringmode3_laddermode1_ringfinder1_nucleicacidmode0.png|cartoon_ring_mode,3|thumb]]<br />
|}<br />
<center>all with defaults:&nbsp;<i>cartoon_ladder_mode,1&nbsp;&nbsp;&nbsp;cartoon_nucleic_acid_mode,0&nbsp;&nbsp;&nbsp;cartoon_ring_finder,1</i></center><br />
== cartoon ladder modes ==<br />
<source lang="python"><br />
set cartoon_ladder_mode, 0 # no ladder<br />
set cartoon_ladder_mode, 1 # with ladder, as stick (if ring mode 0) or link to ring (if rings)<br />
</source><br />
note that the visibility of the ladder sticks depends on ring mode >0, ring finder >0, nucleic acid mode = 0<br />
{|<br />
|[[Image:DNAcartoon_ringfinder1_ringmode3_laddermode0_nucleicacidmode0.png|cartoon_ladder_mode,0|thumb]]<br />
|[[Image:DNAcartoon_ringfinder3_ringmode3_laddermode1_nucleicacidmode0.png|cartoon_ladder_mode,1|thumb]]<br />
|}<br />
all with:&nbsp;<i>cartoon_ring_mode,3&nbsp;&nbsp;&nbsp;cartoon_nucleic_acid_mode,0&nbsp;&nbsp;&nbsp;cartoon_ring_finder,1</i><br />
== cartoon nucleic acid modes ==<br />
<source lang="python"><br />
set cartoon_nucleic_acid_mode, 0 # backbone follow phosphates (red)<br />
set cartoon_nucleic_acid_mode, 1 # backbone follows C4' of ribose (green)<br />
</source><br />
{|<br />
|[[Image:DNAcartoon_ringfinder1_ringmode3_laddermode0_nucleicacidmode0.png|cartoon_nucleic_acid_mode,0|thumb]]<br />
|[[Image:DNAcartoon_ringfinder1_ringmode3_laddermode0_nucleicacidmode1.png|cartoon_nucleic_acid_mode,1|thumb]]<br />
|}<br />
all with:&nbsp;<i>cartoon_ladder_mode,0&nbsp;&nbsp;&nbsp;cartoon_ring_mode,3&nbsp;&nbsp;&nbsp;cartoon_ring_finder,1</i><br />
== cartoon ring finder ==<br />
<source lang="python"><br />
set cartoon_ring_finder, 0 # no ribose, base (or ladder)<br />
set cartoon_ring_finder, 1 # ribose and base ring<br />
set cartoon_ring_finder, 2 # base ring only<br />
</source><br />
{|<br />
|[[Image:DNAcartoon_ringfinder0_ringmode3_laddermode1_nucleicacidmode0.png|cartoon_ring_finder,0|thumb]]<br />
|[[Image:DNAcartoon_ringfinder1_ringmode3_laddermode1_nucleicacidmode0.png|cartoon_ring_finder,1|thumb]]<br />
|[[Image:DNAcartoon_ringfinder2_ringmode3_laddermode1_nucleicacidmode0.png|cartoon_ring_finder,2|thumb]]<br />
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all with:&nbsp;<i>cartoon_ladder_mode,1&nbsp;&nbsp;&nbsp;cartoon_ring_mode,3&nbsp;&nbsp;&nbsp;cartoon_nucleic_acid_mode,0</i></div>Aflaushttps://pymolwiki.org/index.php?title=File:DNAcartoon_ringfinder2_ringmode3_laddermode1_nucleicacidmode0.png&diff=3298File:DNAcartoon ringfinder2 ringmode3 laddermode1 nucleicacidmode0.png2005-11-10T20:11:14Z<p>Aflaus: DNAcartoon_ringfinder2_ringmode3_laddermode1_nucleicacidmode0</p>
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<div>DNAcartoon_ringfinder2_ringmode3_laddermode1_nucleicacidmode0</div>Aflaushttps://pymolwiki.org/index.php?title=File:DNAcartoon_ringfinder1_ringmode3_laddermode1_nucleicacidmode0.png&diff=3297File:DNAcartoon ringfinder1 ringmode3 laddermode1 nucleicacidmode0.png2005-11-10T20:10:49Z<p>Aflaus: DNAcartoon_ringfinder1_ringmode3_laddermode1_nucleicacidmode0</p>
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<div>DNAcartoon_ringfinder1_ringmode3_laddermode1_nucleicacidmode0</div>Aflaushttps://pymolwiki.org/index.php?title=File:DNAcartoon_ringfinder0_ringmode3_laddermode1_nucleicacidmode0.png&diff=3296File:DNAcartoon ringfinder0 ringmode3 laddermode1 nucleicacidmode0.png2005-11-10T20:10:10Z<p>Aflaus: DNAcartoon_ringfinder0_ringmode3_laddermode1_nucleicacidmode0</p>
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<div>DNAcartoon_ringfinder0_ringmode3_laddermode1_nucleicacidmode0</div>Aflaushttps://pymolwiki.org/index.php?title=File:DNAcartoon_ringfinder1_ringmode3_laddermode0_nucleicacidmode1.png&diff=3295File:DNAcartoon ringfinder1 ringmode3 laddermode0 nucleicacidmode1.png2005-11-10T20:01:56Z<p>Aflaus: DNAcartoon_ringfinder1_ringmode3_laddermode0_nucleicacidmode1</p>
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<div>DNAcartoon_ringfinder1_ringmode3_laddermode0_nucleicacidmode0</div>Aflaushttps://pymolwiki.org/index.php?title=File:DNAcartoon_ringmode3_laddermode1_ringfinder1_nucleicacidmode0.png&diff=3292File:DNAcartoon ringmode3 laddermode1 ringfinder1 nucleicacidmode0.png2005-11-10T19:36:24Z<p>Aflaus: DNAcartoon_ringmode3_laddermode1_ringfinder1_nucleicacidmode0</p>
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<div>DNAcartoon_ringmode1_laddermode1_ringfinder1_nucleicacidmode0</div>Aflaushttps://pymolwiki.org/index.php?title=File:DNAcartoon_ringmode0_laddermode1_ringfinder1_nucleicacidmode0.png&diff=3289File:DNAcartoon ringmode0 laddermode1 ringfinder1 nucleicacidmode0.png2005-11-10T19:09:39Z<p>Aflaus: DNAcartoon_ringmode0_laddermode1_ringfinder1_nucleicacidmode0</p>
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