Git install scripts

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/Pymol-script-repo
/home/YOURNAME/Pymol-script-repo

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
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/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.

PyMOL has since revision 3997 (30/04/21012) an improved plugin/script manager. You have to remove old installations of plugins first, to get the automatic plugin installation to work.

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_git = os.path.abspath(os.path.join(os.path.expanduser('~'), 'Pymol-script-repo'))
os.environ['PYMOL_GIT_MOD'] = os.path.join(pymol_git,'modules')
sys.path.append(pymol_git)
sys.path.append(os.environ['PYMOL_GIT_MOD'])

# Make starting directory and change to it.
home_dir = os.path.abspath(os.path.join(os.path.expanduser('~'), 'pymol'))
if not os.path.exists(home_dir): os.makedirs(home_dir)
os.chdir(home_dir)

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_git = os.path.abspath(os.path.join(os.environ['PYMOL_PATH'], 'Pymol-script-repo'))
os.environ['PYMOL_GIT_MOD'] = os.path.join(pymol_git,'modules')
sys.path.append(pymol_git)
sys.path.append(os.environ['PYMOL_GIT_MOD'])

# Make starting directory and change to it.
home_dir = os.path.abspath(os.path.join(os.path.expanduser('~'), 'pymol'))
if not os.path.exists(home_dir): os.makedirs(home_dir)
os.chdir(home_dir)

# Make setting changes to Plugin Manager
import pymol.plugins
pymol.plugins.preferences = {'instantsave': False, 'verbose': False}
pymol.plugins.autoload = {'apbs_tools': False}
pymol.plugins.set_startup_path([os.path.join(pymol_git, 'plugins'), os.path.join(sys.prefix, 'Lib', 'site-packages', 'pmg_tk', 'startup')])
pymol.plugins.preferences = {'instantsave': True, 'verbose': False}

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!
http://www.pymolwiki.org/index.php/git_authors