CCTBX: Difference between revisions

From PyMOLWiki
Jump to navigation Jump to search
No edit summary
No edit summary
Line 1: Line 1:
=Note=
=Note=
We need someone to make some edits to this page.  I don't know anything about CCTBX except what's shown here.
We need someone to make some edits to this page.  I don't know anything about cctbx except what's shown here.


=Computational Crystallography Toolbox=
=Computational Crystallography Toolbox=
[http://cctbx.sourceforge.net CCTBX]
[http://cctbx.sourceforge.net cctbx]


==Using With PyMol==
==Using With PyMol==


===On a Mac===
===On a Mac===
There is a page on the cctbx with special instructions for using it on the Mac [http://cci.lbl.gov/cctbx_build/mac_os_x_notes.html CCTBX On Mac].  Note that you need to use the "Framework" build of PyMOL [http://delsci.com/frameworkpymol/ FrameWorkPyMol].
There is a page on the cctbx with special instructions for using it on the Mac [http://cci.lbl.gov/cctbx_build/mac_os_x_notes.html cctbx On Mac].  Note that you need to use the "Framework" build of PyMOL [http://delsci.com/frameworkpymol/ FrameWorkPyMol].


===Roger Dodd's Solution===
===Windows XP (Roger Dodd)===
Some folks were having issues getting CCTBX to work.  Here's one solution.
1. Download and install python (to the default location - C:\Python24)


I hesitated to post this because I thought someone would have a more elegant solution, but I have got the draw_cell/symmops scripts working
[http://www.python.org/ftp/python/2.4.1/python-2.4.1.msi Python-2.4.1]
on windows with cctbx. I have had it working with all versions of PyMOL including the latest betas. I install PyMOL as usual in '''C:\Program
Files\Delano Scientific\PyMOL'''. I also got hold of python 2.4.1 [http://www.python.org/ftp/python/2.4.1/python-2.4.1.msi Python 2.4.1] and cctbx
[http://cci.lbl.gov/cctbx_build/results/2005_08_18_0201/cctbx_win_xp_py24_pre.exe CCTBX For Windows With Python 2.4] and installed them to '''C:\python24''' and ''''C:\cctbx_build''' & '''C:\cctbx_sources''', respectively.


In order to get things working together, I launch PyMOL with the following batch file:
1a. If you want to use the draw_symops.py or draw_symops_cctbx.py
scripts you also need to install numarray after installing python


<pre>
[http://prdownloads.sourceforge.net/numpy/numarray-1.3.3.win32-py2.4.exe?download Numarray-1.3.3]
@ECHO off
set LIBTBX_DIST_ROOT=C:\cctbx_sources
if not defined PYTHONPATH set PYTHONPATH=
set
PYTHONPATH=C:\cctbx_sources\boost_adaptbx;C:\cctbx_sources\scitbx;C:\cctbx_sources\cctbx;C:\cctbx_sources\iotbx;C:\cctbx_build\libtbx;C:\cctbx_sources\libtbx;%PYTHONPATH%
set LIBTBX_BUILD=C:\cctbx_build
set LIBTBX_PYTHON_EXE=C:\Python24\python.exe
if not defined PATH set PATH=
set PATH=C:\cctbx_build\libtbx\bin;C:\cctbx_build\libtbx;%PATH%
set SCITBX_DIST=C:\cctbx_sources\scitbx
set IOTBX_DIST=C:\cctbx_sources\iotbx
set CCTBX_DIST=C:\cctbx_sources\cctbx
set BOOST_ADAPTBX_DIST=C:\cctbx_sources\boost_adaptbx
set LIBTBX_DIST=C:\cctbx_sources\libtbx
if not defined PATHEXT set PATHEXT=
set PATHEXT=.PX;.PY;%PATHEXT%
call "%LIBTBX_PYTHON_EXE%" "%LIBTBX_DIST%\libtbx\assoc_ftype.py"
"C:\Program Files\DeLano Scientific\PyMOL\PyMOLWin.exe"  +2
</pre>


Just save as '''PyMOL.bat''' and run it (this is basically the cctbx '''setpaths.bat''' with a pymol command tagged on the end). I hope this helps.
2. Download cctbx *without* python included and unpack into
C:\cctbx_build and C:\cctbx_sources


[http://cci.lbl.gov/cctbx_build/results/2005_08_18_0201/cctbx_win_xp_py24_pre.exe cctbx]


3. Download pymol built against python 2.4 (but not including its own
python) and install in the default location


=== Robert Campbell's Solution ===
[http://delsci.com/rel/0_98/pymol-0_98rc5-bin-win32-py24.zip pymol-0_98rc5]
 
(You cannot use the latest beta versions which include their own version
of python to the best of my knowledge)
 
4. Create 2 files (use notepad or wordpad or any other text editor) and
save in the C:\Program Files\Delano Scientific\PyMOL directory:
 
    a) pymol.cmd
 
      @python -x "%~f0" %* & exit /b
        import cctbx
        import pymol
 
    b) run.cmd
 
        CALL C:\cctbx_build\setpaths_all.bat
        CALL "C:\Program Files\Delano Scientific\PyMOL\pymol.cmd"
 
5. One other thing, it's important to have python in your path variable
(which you can access by going to control
panel|system|advanced|environment variables), just add C:\python24 to
the end of the path variable, separated by a semi-colon.
 
===Linux (Robert Campbell)===
When you run the setpaths.sh script, it adds the cctbx_build/bin directory to the *front* of your $PATH. In that directory is a shell script called "python" that sets the environment necessary to import cctbx. So, to get cctbx to work, you have to call python without prefixing a directory path.  If you were like me and had:
When you run the setpaths.sh script, it adds the cctbx_build/bin directory to the *front* of your $PATH. In that directory is a shell script called "python" that sets the environment necessary to import cctbx. So, to get cctbx to work, you have to call python without prefixing a directory path.  If you were like me and had:
  /usr/bin/python  $PYMOL_PATH/modules/launch_pymol.py $*
  /usr/bin/python  $PYMOL_PATH/modules/launch_pymol.py $*

Revision as of 05:13, 20 September 2005

Note

We need someone to make some edits to this page. I don't know anything about cctbx except what's shown here.

Computational Crystallography Toolbox

cctbx

Using With PyMol

On a Mac

There is a page on the cctbx with special instructions for using it on the Mac cctbx On Mac. Note that you need to use the "Framework" build of PyMOL FrameWorkPyMol.

Windows XP (Roger Dodd)

1. Download and install python (to the default location - C:\Python24)

Python-2.4.1

1a. If you want to use the draw_symops.py or draw_symops_cctbx.py scripts you also need to install numarray after installing python

Numarray-1.3.3

2. Download cctbx *without* python included and unpack into C:\cctbx_build and C:\cctbx_sources

cctbx

3. Download pymol built against python 2.4 (but not including its own python) and install in the default location

pymol-0_98rc5

(You cannot use the latest beta versions which include their own version of python to the best of my knowledge)

4. Create 2 files (use notepad or wordpad or any other text editor) and save in the C:\Program Files\Delano Scientific\PyMOL directory: 

   a) pymol.cmd

      @python -x "%~f0" %* & exit /b
       import cctbx
       import pymol

   b) run.cmd

       CALL C:\cctbx_build\setpaths_all.bat
       CALL "C:\Program Files\Delano Scientific\PyMOL\pymol.cmd"

5. One other thing, it's important to have python in your path variable (which you can access by going to control panel|system|advanced|environment variables), just add C:\python24 to the end of the path variable, separated by a semi-colon.

Linux (Robert Campbell)

When you run the setpaths.sh script, it adds the cctbx_build/bin directory to the *front* of your $PATH. In that directory is a shell script called "python" that sets the environment necessary to import cctbx. So, to get cctbx to work, you have to call python without prefixing a directory path. If you were like me and had: 

/usr/bin/python  $PYMOL_PATH/modules/launch_pymol.py $*

in your pymol.com file, then it would not run that cctbx_build/bin/python script. So you need to either change the above line to: 

python  $PYMOL_PATH/modules/launch_pymol.py $*

(assuming you've already run the setpaths.sh script) or you need to copy the cctbx_build/bin/python contents (without the actual "python" command) into your pymol.com file or some other file that you source before pymol.com.

Within pymol, type the command: 

print sys.path

and you should now see the cctbx directories show up.


I hope this is clear enough!

Retrieved from "https://pymolwiki.org/index.php?title=CCTBX&oldid=1083"