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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. | ||
Now unpack the files to a directory. For example: | Now unpack the files to a directory. For example: | ||
− | C:/Users/YOURNAME | + | C:/Users/YOURNAME/Pymol-script-repo |
− | + | /home/YOURNAME/Pymol-script-repo | |
− | /home/YOURNAME/ | ||
− | + | Continue with [[#Adding Pymol-script-repo to PyMOL search path]] | |
== Git install instructions == | == Git install instructions == | ||
− | === For | + | === For Windows users === |
# Install [http://code.google.com/p/msysgit/downloads/list?can=3&q=official+Git Git for Windows]. | # Install [http://code.google.com/p/msysgit/downloads/list?can=3&q=official+Git Git for Windows]. | ||
Use following settings in options, [http://www.geekgumbo.com/2010/04/09/installing-git-on-windows/ (You can read more here)]. | Use following settings in options, [http://www.geekgumbo.com/2010/04/09/installing-git-on-windows/ (You can read more here)]. | ||
Line 18: | Line 17: | ||
* Checkout Windows style, commit Unix-style endings | * Checkout Windows style, commit Unix-style endings | ||
− | # Navigate to: '''C: | + | # Navigate to: '''C:\Users\YOURNAME''' |
# Right click in folder -> Select: Git Gui -> Clone Existing Repository | # Right click in folder -> Select: Git Gui -> Clone Existing Repository | ||
# Source Location: git://github.com/Pymol-Scripts/Pymol-script-repo.git | # Source Location: git://github.com/Pymol-Scripts/Pymol-script-repo.git | ||
− | # Target Directory: C: | + | # Target Directory: C:\\Users\\YOURNAME\\Pymol-script-repo |
+ | #: A backslash "\" in a string is [http://effbot.org/pyref/string-literals.htm 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. | You now have all the scripts available in your directory. | ||
− | === For | + | === For Linux users === |
# Install git | # Install git | ||
+ | # Debian/Ubuntu/Mint | ||
sudo apt-get install git | sudo apt-get install git | ||
+ | # Fedora | ||
+ | su -c 'yum install git' | ||
+ | # openSUSE | ||
+ | sudo zypper in git | ||
+ | |||
# Navigate to desired folder: | # Navigate to desired folder: | ||
− | cd /home/YOURNAME/ | + | cd /home/YOURNAME/ |
git clone git://github.com/Pymol-Scripts/Pymol-script-repo.git | git clone git://github.com/Pymol-Scripts/Pymol-script-repo.git | ||
− | You now have all the scripts available in: /home/YOURNAME | + | You now have all the scripts available in: /home/YOURNAME/Pymol-script-repo |
== Adding Pymol-script-repo to PyMOL search path == | == Adding Pymol-script-repo to PyMOL search path == | ||
− | 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. |
− | === | + | |
− | # Open notepad | + | === 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''' | |
− | + | <syntaxhighlight lang="python"> | |
+ | # 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 | ||
+ | </syntaxhighlight> | ||
+ | |||
+ | 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.<br> | ||
+ | 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> | ||
+ | Write in "run_on_startup.py" : | ||
+ | <syntaxhighlight lang="python"> | ||
+ | # 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) | |
+ | </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 == | ||
If new scripts are available or changes have been made, then: | If new scripts are available or changes have been made, then: | ||
=== For windows users === | === For windows users === | ||
− | # Navigate to '''C: | + | # Navigate to '''C:\Users\YOURNAME\Pymol-script-repo''' |
# Right click in folder -> Select: Git Bash | # Right click in folder -> Select: Git Bash | ||
# Write in terminal | # Write in terminal | ||
git pull origin master | git pull origin master | ||
+ | |||
=== For Ubuntu/Mint users === | === For Ubuntu/Mint users === | ||
− | # Navigate to '''/home/YOURNAME | + | # Navigate to '''/home/YOURNAME/Pymol-script-repo''' |
# Write in terminal. | # Write in terminal. | ||
git pull origin master | git pull origin master | ||
Line 68: | 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]