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Difference between revisions of "Git install scripts"
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== Manual download of scripts == | == Manual download of scripts == | ||
− | If you don't have the option or | + | 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. | ||
Line 7: | Line 7: | ||
/home/YOURNAME/Pymol-script-repo | /home/YOURNAME/Pymol-script-repo | ||
− | + | Continue with [[#Adding Pymol-script-repo to PyMOL search path]] | |
== Git install instructions == | == Git install instructions == | ||
Line 41: | Line 41: | ||
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. | ||
− | |||
− | |||
=== Making a personal "pymolrc" file - for personal use === | === Making a personal "pymolrc" file - for personal use === | ||
# Open notepad/gedit and save under: | # Open notepad/gedit and save under: | ||
Line 50: | Line 48: | ||
# Add paths to sys.path so PyMOL can find modules and scripts | # Add paths to sys.path so PyMOL can find modules and scripts | ||
import sys, os | import sys, os | ||
− | + | pymol_script_repo = os.path.abspath(os.path.join(os.path.expanduser('~'), 'Pymol-script-repo')) | |
− | os. | + | pymol_script_repo_plugins = os.path.join(pymol_script_repo, "plugins") |
− | sys.path.append( | + | pymol_script_repo_modules = os.path.join(pymol_script_repo, "modules") |
− | sys.path.append(os.environ['PYMOL_GIT_MOD'] | + | sys.path.append(pymol_script_repo) |
− | + | sys.path.append(pymol_script_repo_modules) | |
− | + | os.environ['PYMOL_GIT_MOD'] = pymol_script_repo_modules | |
− | |||
− | |||
− | |||
</syntaxhighlight> | </syntaxhighlight> | ||
Line 67: | Line 62: | ||
=== Making a general "run_on_startup.py" - for all users === | === 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> | 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: | First locate your PYMOL_PATH. Start PyMOL, and write: | ||
− | + | ||
− | + | <syntaxhighlight lang="python"> | |
+ | import os | ||
+ | print(os.environ['PYMOL_PATH']) | ||
+ | </syntaxhighlight> | ||
+ | |||
In this folder, you place "run_on_startup.py" and the Pymol-script-repo directory.<br> | In this folder, you place "run_on_startup.py" and the Pymol-script-repo directory.<br> | ||
Write in "run_on_startup.py" : | Write in "run_on_startup.py" : | ||
Line 76: | Line 76: | ||
# Add paths to sys.path so PyMOL can find modules and scripts | # Add paths to sys.path so PyMOL can find modules and scripts | ||
import sys, os | import sys, os | ||
− | + | pymol_script_repo = os.path.abspath(os.path.join(os.environ['PYMOL_PATH'], 'Pymol-script-repo')) | |
− | os. | + | pymol_script_repo_plugins = os.path.join(pymol_script_repo, "plugins") |
− | sys.path.append( | + | pymol_script_repo_modules = os.path.join(pymol_script_repo, "modules") |
− | sys.path.append(os.environ['PYMOL_GIT_MOD'] | + | 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 | # Make setting changes to Plugin Manager | ||
import pymol.plugins | import pymol.plugins | ||
− | pymol.plugins. | + | pymol.plugins.autoload['apbs_tools'] = False |
− | pymol.plugins. | + | pymol.plugins.preferences['verbose'] = False |
− | pymol.plugins. | + | _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. | ||
− | + | ||
− | + | <syntaxhighlight lang="python"> | |
− | + | print(sys.path) | |
+ | import colorbydisplacement | ||
+ | help(colorbydisplacement) | ||
+ | </syntaxhighlight> | ||
== Get latest changes to scripts == | == Get latest changes to scripts == | ||
Line 115: | 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> | ||
− | + | [git authors] |
Latest revision as of 03:24, 10 December 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
- 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
- Navigate to: C:\Users\YOURNAME
- Right click in folder -> Select: Git Gui -> Clone Existing Repository
- Source Location: git://github.com/Pymol-Scripts/Pymol-script-repo.git
- 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
- Install git
# Debian/Ubuntu/Mint sudo apt-get install git # Fedora su -c 'yum install git' # openSUSE sudo zypper in git
- 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
- Open notepad/gedit and save under:
- Win: C:\Users\YOURNAME\pymolrc.pym (Set: "Save as type" to "All files")
- 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
- 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.
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
- Navigate to C:\Users\YOURNAME\Pymol-script-repo
- Right click in folder -> Select: Git Bash
- Write in terminal
git pull origin master
For Ubuntu/Mint users
- Navigate to /home/YOURNAME/Pymol-script-repo
- 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]