Git install scripts

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]