Git install scripts

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Revision as of 14:58, 9 December 2011 by Tlinnet (talk | contribs) (Adding Pymol-script-repo to PyMOL search path)
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Manual download of scripts

If you don't have the option or want't to install 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/Documents/Pymol-script-repo

or

/home/YOURNAME/Software/pymol

Now go to: Adding Pymol-script-repo to PyMOL search path [1]

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\Documents
  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\\Documents\\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 Ubuntu/Mint users

  1. Install git
sudo apt-get install git
  1. Navigate to desired folder:
cd /home/YOURNAME/Software/pymol
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

Adding Pymol-script-repo to 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
This is activated with: import plugins.
You have to remove old installations of plugins first, to get the automatic plugin installation to work.

For windows users

  1. Open notepad
  2. Write (Remember double backslashes)
import sys,os
sys.path.append('C:\\Users\\YOURNAME\\Documents\\pymol\\Pymol-script-repo')
import plugins
os.chdir('C:\\Users\\YOURNAME\\Documents\\pymol')                                # Your standard working dir

Save under: C:\Users\YOURNAME\pymolrc.pym (Set: "Save as type" to "All files")

For Ubuntu/Mint users

gedit ~/.pymolrc

Write

import sys,os
sys.path.append('/home/YOURNAME/Software/pymol/Pymol-script-repo')
import plugins
os.chdir('/home/YOURNAME/Software/pymol/')                                      # Your standard working dir

Save and exit

Adding Pymol-script-repo/modules to PYTHONPATH

Some PyMOL plugins (ex, autodock_plugin,Apbsplugin executes external python scripts, which depends on modules.
These modules can already be part of your installation, but as a convenience, they have also been packed into Pymol-script-repo/modules.
When calling external python scripts, we need to be sure, that they can locate these modules. We do this by setting the PYTHONPATH.

For windows users

For Ubuntu/Mint users

gedit ~/.bash_profile

Write

source ~/.bashrc

Then

gedit ~/.bashrc

Write

PYTHONPATH=$PYTHONPATH:/home/YOU/Software/pymol/Pymol-script-repo/modules
export PYTHONPATH

Save and exit, logout, and login. Test by writing in terminal.

env
python
>>> import sys
>>> print sys.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\Documents\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/Software/pymol/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!
http://www.pymolwiki.org/index.php/git_authors