Plugin Manager

Newer versions of PyMOL come with a Plugin Manager, which can be used to load plugins such as those in the PyMOL Script Repo.

Manual Setup

In the PyMOL menu naviagte to Plugins > Plugin Manager
Here you can manually add directories or scripts that will be loaded upon startup.
Older versions have a basic version of this manager: Plugin > Manage Plugins, however, here the scripts need to be added individually.

Scripted setup during PyMOL launching

Creating run_on_startup.py

run_on_startup.py can easily be created using a text editor such as notepad.

The run_on_startup.py is handled similar to pymolrc files and is executed every time PyMOL launches.
An important distinction is that run_on_startup.py is executed before the pymolrc files and is purely written in python.
The recommended location of run_on_startup.py is the PyMOL home directory (PYMOL_PATH, e.g. something like 'C:\Program Files \PyMOL\').
An advantage is that should PyMOL be installed on a computer with several users, this will be run for all users, while the pymolrc files can be individual (e.g. in the USER directory).

#this can be copy-pasted to create run_on_startup.py in the home directory
 
# Add paths to sys.path so PyMOL can find modules and scripts
import sys
import os
 
pymol_git = os.path.realpath(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 setting changes to Plugin Manager
try: # in case the PyMOL is older and doe not have the module pymol.plugins
    import pymol.plugins
 
    #THIS IS WHERE THE PATH IS ADDED TO INITIALIZE PLUGINS USING THE PLUGIN MANAGER
    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': False, 'verbose': False}
    pymol.plugins.autoload = {'apbs_tools': False}
    pymol.plugins.preferences = {'instantsave': True, 'verbose': False}
    # This can be used to trace if PyMOL executed the file correctly
    print 'Loaded run_on_stratup.py'
except:
    print 'NB! Plugin Manager not present!'

Note that this block will also add the Pymol-script-repo and the subfolder Pymol-script-repo/modules to PyMOL's search path.
This is something that is required in earlier PyMOL version to allow import of scripts. Thus this version of run_on_startup.py can be used for older versions, too.
Note that the settings specific for the new version of the Plugin Manager will not have an effect.

What if the 'Pymol-script-repo' is not in the PyMOL directory?

If the Pymol-script-repo is located somewhere else the first section of the run_on_startup.py file will be different.
E.g. in the USER directory:

# This would replace the first section in '''run_on_startup.py'''.
import sys
import 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'])

E.g. in any other path:

# This would replace the first section in '''run_on_startup.py'''.
import sys
import os

pymol_git = os.path.realpath('D:/MY/RANDOM/PATH/TO/Pymol-script-repo') # Adjust this line
# Note the slash ('/') instead of backslash ('\'), beware Windows users!

os.environ['PYMOL_GIT_MOD'] = os.path.join(pymol_git,'modules')
sys.path.append(pymol_git)
sys.path.append(os.environ['PYMOL_GIT_MOD'])

Appending additional paths to the Plugin Manager

Should your scripts be located in several alternative locations, it is possible to append additional directories to the Plugin Manager.
In the example below, a directory called 'plugins_private', which is located in the PyMOL directory, is added to the Plugin Manger.
Should the folder be somewhere else the example below can be adjusted as outlined above.

#copy paste into PyMOL's command line or into the pymolrc

python
import os
import sys
import pymol.plugins # Note that this requires the 'new' Plugin Manager

PRIVATE_PATH=os.path.realpath(os.path.join(os.environ['PYMOL_PATH'], 'plugins_private'))
startupdirectories=list(pymol.plugins.get_startup_path(True))
if PRIVATE_PATH not in startupdirectories:
    startupdirectories.append(PRIVATE_PATH)
if PRIVATE_PATH not in sys.path:
    sys.path.append(PRIVATE_PATH)
pymol.plugins.set_startup_path(startupdirectories)
python end

Note that the Plugin Manager supports loading entire folders with scripts ('modules').
If you have such a folder, make sure it contains a file called '__init__.py', which can be empty.

If you don't have a Plugin Manager

If you are running an older PyMOL without Plugin Manager you can either upgrade to the newest version or load plugins the traditional way.
For detailed instructions see: Git install scripts
Essentially, make sure that the folder is added to PyMOL's search paths.

import sys
import os
pymol_git = os.path.realpath(os.path.join(os.environ['PYMOL_PATH'], 'Pymol-script-repo'))
sys.path.append(pymol_git)

Import a plugin manually:

# EXAMPLE
delete all
frag LYS
cgo_arrow name N, name O # will not work if 'cgo_arrow' is not loaded

import cgo_arrow # PyMOL will look for this file and load it
cgo_arrow name N, name O # should work if it is loaded

SEE ALSO

Git install scripts