Difference between revisions of "Git install scripts"

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(For Linux users: added alternative version of the .pymolrc text for username-agnostic version)
(remove stuff like "Make starting directory")
 
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== Manual download of scripts ==
 
== Manual download of scripts ==
If you don't have the option or want't to install git on your system, then go to
+
If you don't have the option or don't feel like installing git on your system, then go to:
 
  https://github.com/Pymol-Scripts/Pymol-script-repo
 
  https://github.com/Pymol-Scripts/Pymol-script-repo
 
Click the "ZIP" button, near the top left corner.
 
Click the "ZIP" button, near the top left corner.
 
Now unpack the files to a directory. For example:
 
Now unpack the files to a directory. For example:
  C:/Users/YOURNAME/Documents/Pymol-script-repo
+
  C:/Users/YOURNAME/Pymol-script-repo
or
+
  /home/YOURNAME/Pymol-script-repo
  /home/YOURNAME/Software/pymol
 
  
Now go to: '''Adding Pymol-script-repo to PyMOL search path''' [http://www.pymolwiki.org/index.php/Git_install#Adding_Pymol-script-repo_to_PyMOL_search_path]
+
Continue with [[#Adding Pymol-script-repo to PyMOL search path]]
  
 
== Git install instructions ==
 
== Git install instructions ==
Line 18: Line 17:
 
* Checkout Windows style, commit Unix-style endings
 
* Checkout Windows style, commit Unix-style endings
  
# Navigate to: '''C:\Users\YOURNAME\Documents\pymol'''
+
# Navigate to: '''C:\Users\YOURNAME'''
 
# Right click in folder -> Select: Git Gui -> Clone Existing Repository
 
# Right click in folder -> Select: Git Gui -> Clone Existing Repository
 
# Source Location: git://github.com/Pymol-Scripts/Pymol-script-repo.git
 
# Source Location: git://github.com/Pymol-Scripts/Pymol-script-repo.git
# Target Directory: C:\\Users\\YOURNAME\\Documents\\pymol\Pymol-script-repo
+
# Target Directory: C:\\Users\\YOURNAME\\Pymol-script-repo
 
#: A backslash "\" in a string is [http://effbot.org/pyref/string-literals.htm is used for escape sequences]. To get a real backslash in a string, use double backslash "\\"   
 
#: A backslash "\" in a string is [http://effbot.org/pyref/string-literals.htm is used for escape sequences]. To get a real backslash in a string, use double backslash "\\"   
 
You now have all the scripts available in your directory.
 
You now have all the scripts available in your directory.
 
Add '''python.exe''' to your '''PATH''', so external .py scripts can be executed.<br>
 
Open control panel. Search for, and click: '''Edit environment variables for your account'''<br>
 
Add to end of variable PATH: ''';C:\Python27'''  (Or other path to your python python.exe)<br>
 
Click start button, and open '''cmd.exe'''. Try starting python by writing: '''python'''
 
  
 
=== For Linux users ===
 
=== For Linux users ===
Line 40: Line 34:
  
 
# Navigate to desired folder:  
 
# Navigate to desired folder:  
  cd /home/YOURNAME/Software/pymol
+
  cd /home/YOURNAME/
 
  git clone git://github.com/Pymol-Scripts/Pymol-script-repo.git
 
  git clone git://github.com/Pymol-Scripts/Pymol-script-repo.git
You now have all the scripts available in: /home/YOURNAME/Software/pymol/Pymol-script-repo
+
You now have all the scripts available in: /home/YOURNAME/Pymol-script-repo
  
 
== Adding Pymol-script-repo to PyMOL search path ==
 
== Adding Pymol-script-repo to PyMOL search path ==
 
You now have to add the "Pymol-script-repo" directory to the PyMOL search path.  
 
You now have to add the "Pymol-script-repo" directory to the PyMOL search path.  
  
The project also have automatically plugin installer: http://www.pymolwiki.org/index.php/plugindirectory <br>
+
=== Making a personal "pymolrc" file - for personal use ===
This is activated with: '''import plugins'''. <br>
+
# Open notepad/gedit and save under:
'''You have to remove old installations of plugins first, to get the automatic plugin installation to work.'''
+
## Win: '''C:\Users\YOURNAME\pymolrc.pym''' (Set: "Save as type" to "All files")
=== For Windows users ===
+
## Linux: '''~/.pymolrc'''
# Open notepad
+
<syntaxhighlight lang="python">
# Write (Remember double backslashes)
+
# Add paths to sys.path so PyMOL can find modules and scripts
import sys,os
+
import sys, os
sys.path.append('C:\\Users\\YOURNAME\\Documents\\pymol\\Pymol-script-repo')
+
pymol_script_repo = os.path.abspath(os.path.join(os.path.expanduser('~'), 'Pymol-script-repo'))
os.environ['PYMOL_GIT_MOD']='C:\\Users\\YOURNAME\\Documents\\pymol\\Pymol-script-repo\\modules'
+
pymol_script_repo_plugins = os.path.join(pymol_script_repo, "plugins")
import plugins
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pymol_script_repo_modules = os.path.join(pymol_script_repo, "modules")
os.chdir('C:\\Users\\YOURNAME\\Documents\\pymol')                                # Your standard working dir
+
sys.path.append(pymol_script_repo)
Save under: '''C:\Users\YOURNAME\pymolrc.pym''' (Set: "Save as type" to "All files")
+
sys.path.append(pymol_script_repo_modules)
 +
os.environ['PYMOL_GIT_MOD'] = pymol_script_repo_modules
 +
</syntaxhighlight>
 +
 
 +
Then open PyMOL. Go to top menu: Plugin->Plugin Manager
 +
# Installed plugins: Unclick "apbs_tools" as "load on startup". (The Pymol-script-repo has a fine-tuned version, "apbsplugin")
 +
# Settings->Add new directory: Point to: /custom/path/Pymol-script-repo/plugins
 +
# Restart PyMOL
 +
 
 +
=== Making a general "run_on_startup.py" - for all users ===
 +
 
 +
If you have a shared PyMOL installation for several linux computers, you can make general wide changes for the startup of PyMOL.<br>
 +
First locate your PYMOL_PATH. Start PyMOL, and write:
  
=== For Linux users ===
 
gedit ~/.pymolrc
 
Write
 
 
<syntaxhighlight lang="python">
 
<syntaxhighlight lang="python">
import sys,os
+
import os
sys.path.append('/home/YOU/Software/pymol/Pymol-script-repo')
+
print(os.environ['PYMOL_PATH'])
os.environ['PYMOL_GIT_MOD']='/home/YOU/Software/pymol/Pymol-script-repo/modules'
 
import plugins
 
os.chdir('/home/YOU/Software/pymol/')                             # Your standard working dir
 
 
</syntaxhighlight>
 
</syntaxhighlight>
Save and exit
 
  
==== Alternative ====
+
In this folder, you place "run_on_startup.py" and the Pymol-script-repo directory.<br>
Or perhaps insert the following code instead (no need to insert USERNAME, so more generic) <!-- this works for me, but please edit if this is wrong -->
+
Write in "run_on_startup.py" :
 
<syntaxhighlight lang="python">
 
<syntaxhighlight lang="python">
# eventually add ~/Software/pymol/Pymol-script-repo to sys.path
+
# Add paths to sys.path so PyMOL can find modules and scripts
 
import sys, os
 
import sys, os
sys.path.append(os.path.expanduser('~/Software/pymol/Pymol-script-repo'))
+
pymol_script_repo = os.path.abspath(os.path.join(os.environ['PYMOL_PATH'], 'Pymol-script-repo'))
os.environ['PYMOL_GIT_MOD']=os.path.expanduser('~/Software/pymol/Pymol-script-repo')
+
pymol_script_repo_plugins = os.path.join(pymol_script_repo, "plugins")
+
pymol_script_repo_modules = os.path.join(pymol_script_repo, "modules")
# load the module
+
sys.path.append(pymol_script_repo)
import plugins
+
sys.path.append(pymol_script_repo_modules)
 +
os.environ['PYMOL_GIT_MOD'] = pymol_script_repo_modules
 +
 
 +
# Make setting changes to Plugin Manager
 +
import pymol.plugins
 +
pymol.plugins.autoload['apbs_tools'] = False
 +
pymol.plugins.preferences['verbose'] = False
 +
_plugin_search_path = pymol.plugins.get_startup_path()
 +
if pymol_script_repo_plugins not in _plugin_search_path: pymol.plugins.set_startup_path([pymol_script_repo_plugins] + _plugin_search_path)
 
</syntaxhighlight>
 
</syntaxhighlight>
  
 
== Test the Scripts ==
 
== Test the Scripts ==
 
Now start PyMOL, and test in PyMOL.
 
Now start PyMOL, and test in PyMOL.
print sys.path
+
 
import colorbydisplacement
+
<syntaxhighlight lang="python">
help(colorbydisplacement)
+
print(sys.path)
 +
import colorbydisplacement
 +
help(colorbydisplacement)
 +
</syntaxhighlight>
  
 
== Get latest changes to scripts ==
 
== Get latest changes to scripts ==
 
If new scripts are available or changes have been made, then:
 
If new scripts are available or changes have been made, then:
 
=== For windows users ===
 
=== For windows users ===
# Navigate to '''C:\Users\YOURNAME\Documents\Pymol-script-repo'''
+
# Navigate to '''C:\Users\YOURNAME\Pymol-script-repo'''
 
# Right click in folder -> Select: Git Bash
 
# Right click in folder -> Select: Git Bash
 
# Write in terminal
 
# Write in terminal
Line 99: Line 109:
  
 
=== For Ubuntu/Mint users ===
 
=== For Ubuntu/Mint users ===
# Navigate to '''/home/YOURNAME/Software/pymol/Pymol-script-repo'''
+
# Navigate to '''/home/YOURNAME/Pymol-script-repo'''
 
# Write in terminal.
 
# Write in terminal.
 
  git pull origin master
 
  git pull origin master
Line 105: Line 115:
 
= Do you want to contribute with a script? =
 
= Do you want to contribute with a script? =
 
Information how to contribute scripts to the repository. It's easy! <br>
 
Information how to contribute scripts to the repository. It's easy! <br>
http://www.pymolwiki.org/index.php/git_authors
+
[git authors]

Latest revision as of 08:46, 13 November 2018

Manual download of scripts

If you don't have the option or don't feel like installing git on your system, then go to:

https://github.com/Pymol-Scripts/Pymol-script-repo

Click the "ZIP" button, near the top left corner. Now unpack the files to a directory. For example:

C:/Users/YOURNAME/Pymol-script-repo
/home/YOURNAME/Pymol-script-repo

Continue with #Adding Pymol-script-repo to PyMOL search path

Git install instructions

For Windows users

  1. Install Git for Windows.

Use following settings in options, (You can read more here).

  • Windows Explorer Integration -> Context Menu Entries -> Git Bash Here + Git GUI here
  • Run Git and included Unix tools from Windows Command prompts
  • Checkout Windows style, commit Unix-style endings
  1. Navigate to: C:\Users\YOURNAME
  2. Right click in folder -> Select: Git Gui -> Clone Existing Repository
  3. Source Location: git://github.com/Pymol-Scripts/Pymol-script-repo.git
  4. Target Directory: C:\\Users\\YOURNAME\\Pymol-script-repo
    A backslash "\" in a string is is used for escape sequences. To get a real backslash in a string, use double backslash "\\"

You now have all the scripts available in your directory.

For Linux users

  1. Install git
# Debian/Ubuntu/Mint
sudo apt-get install git
# Fedora
su -c 'yum install git'
# openSUSE
sudo zypper in git
  1. Navigate to desired folder:
cd /home/YOURNAME/
git clone git://github.com/Pymol-Scripts/Pymol-script-repo.git

You now have all the scripts available in: /home/YOURNAME/Pymol-script-repo

Adding Pymol-script-repo to PyMOL search path

You now have to add the "Pymol-script-repo" directory to the PyMOL search path.

Making a personal "pymolrc" file - for personal use

  1. Open notepad/gedit and save under:
    1. Win: C:\Users\YOURNAME\pymolrc.pym (Set: "Save as type" to "All files")
    2. Linux: ~/.pymolrc
# Add paths to sys.path so PyMOL can find modules and scripts
import sys, os
pymol_script_repo = os.path.abspath(os.path.join(os.path.expanduser('~'), 'Pymol-script-repo'))
pymol_script_repo_plugins = os.path.join(pymol_script_repo, "plugins")
pymol_script_repo_modules = os.path.join(pymol_script_repo, "modules")
sys.path.append(pymol_script_repo)
sys.path.append(pymol_script_repo_modules)
os.environ['PYMOL_GIT_MOD'] = pymol_script_repo_modules

Then open PyMOL. Go to top menu: Plugin->Plugin Manager

  1. Installed plugins: Unclick "apbs_tools" as "load on startup". (The Pymol-script-repo has a fine-tuned version, "apbsplugin")
  2. Settings->Add new directory: Point to: /custom/path/Pymol-script-repo/plugins
  3. Restart PyMOL

Making a general "run_on_startup.py" - for all users

If you have a shared PyMOL installation for several linux computers, you can make general wide changes for the startup of PyMOL.
First locate your PYMOL_PATH. Start PyMOL, and write:

import os
print(os.environ['PYMOL_PATH'])

In this folder, you place "run_on_startup.py" and the Pymol-script-repo directory.
Write in "run_on_startup.py" :

# Add paths to sys.path so PyMOL can find modules and scripts
import sys, os
pymol_script_repo = os.path.abspath(os.path.join(os.environ['PYMOL_PATH'], 'Pymol-script-repo'))
pymol_script_repo_plugins = os.path.join(pymol_script_repo, "plugins")
pymol_script_repo_modules = os.path.join(pymol_script_repo, "modules")
sys.path.append(pymol_script_repo)
sys.path.append(pymol_script_repo_modules)
os.environ['PYMOL_GIT_MOD'] = pymol_script_repo_modules

# Make setting changes to Plugin Manager
import pymol.plugins
pymol.plugins.autoload['apbs_tools'] = False
pymol.plugins.preferences['verbose'] = False
_plugin_search_path = pymol.plugins.get_startup_path()
if pymol_script_repo_plugins not in _plugin_search_path: pymol.plugins.set_startup_path([pymol_script_repo_plugins] + _plugin_search_path)

Test the Scripts

Now start PyMOL, and test in PyMOL.

print(sys.path)
import colorbydisplacement
help(colorbydisplacement)

Get latest changes to scripts

If new scripts are available or changes have been made, then:

For windows users

  1. Navigate to C:\Users\YOURNAME\Pymol-script-repo
  2. Right click in folder -> Select: Git Bash
  3. Write in terminal
git pull origin master

For Ubuntu/Mint users

  1. Navigate to /home/YOURNAME/Pymol-script-repo
  2. Write in terminal.
git pull origin master

Do you want to contribute with a script?

Information how to contribute scripts to the repository. It's easy!
[git authors]