Git install scripts: Difference between revisions

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= For windows users =
== 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 [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 the default settings in all options.
Use following settings in options, [http://www.geekgumbo.com/2010/04/09/installing-git-on-windows/ (You can read more here)].
# Navigate in your computer to: C:/Users/YOURNAME/Documents  (Note, always use forward slashes "/" for compatibility)
* 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
# Right click in folder -> Select: Git Gui -> Clone Existing Repository
# Source Location: https://github.com/Pymol-Scripts/Pymol-script-repo
# Source Location: git://github.com/Pymol-Scripts/Pymol-script-repo.git
# Target Directory: C:/Users/YOURNAME/Documents/Pymol-script-repo
# 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.


You now have to add the "Pymol-script-repo" directory to the PyMOL search path.
=== For Linux users ===
# Open notepad
# Install git
# Write (Remember forward slashes)
# Debian/Ubuntu/Mint
import sys
sudo apt-get install git
sys.path.append('C:/Users/YOURNAME/Documents/Pymol-script-repo')
# Fedora
Save under: C:/Users/YOURNAME/pymolrc.pym (Set: "Save as type" to "All files")
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'''
<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:


Now start PyMOL, and test in PyMOL.
<syntaxhighlight lang="python">
print sys.path
import os
import colorbydisplacement
print(os.environ['PYMOL_PATH'])
help(colorbydisplacement)
</syntaxhighlight>


= For Ubuntu/Mint users =
In this folder, you place "run_on_startup.py" and the Pymol-script-repo directory.<br>
# Install git
Write in "run_on_startup.py" :  
sudo apt-get install git
<syntaxhighlight lang="python">
# Navigate to desired folder: cd /home/YOURNAME/Software/pymol
# Add paths to sys.path so PyMOL can find modules and scripts
git clone https://github.com/Pymol-Scripts/Pymol-script-repo.git
import sys, os
You now have all the scripts available in: /home/YOURNAME/Software/pymol/Pymol-script-repo
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


You now have to add the "Pymol-script-repo" directory to the PyMOL search path.
# Make setting changes to Plugin Manager
gedit ~/.pymolrc
import pymol.plugins
Write
pymol.plugins.autoload['apbs_tools'] = False
import sys
pymol.plugins.preferences['verbose'] = False
sys.path.append('/home/YOURNAME/Software/pymol/Pymol-script-repo')
_plugin_search_path = pymol.plugins.get_startup_path()
Save and exit
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 ==
Now start PyMOL, and test in PyMOL.
Now start PyMOL, and test in PyMOL.
print sys.path
 
import colorbydisplacement
<syntaxhighlight lang="python">
help(colorbydisplacement)
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:
# Navigate to '''/home/YOURNAME/Software/pymol/Pymol-script-repo'''
=== For windows users ===
# Write '''git pull''' in terminal. Now you are done.
# 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? =
= 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>
http://www.pymolwiki.org/index.php/git_authors
[git authors]

Latest revision as of 07:46, 13 November 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

  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]

Retrieved from "https://pymolwiki.org/index.php?title=Git_install_scripts&oldid=12827"