Git install scripts - Revision history

Cchem: 1 revision

2018-12-10T03:24:45Z

1 revision

Speleo3: remove stuff like "Make starting directory"

2018-11-13T12:46:08Z

remove stuff like "Make starting directory"

Bell: 1 revision

2014-11-26T15:24:26Z

1 revision

Sbliven: Fixing capitalization

2014-11-24T09:22:49Z

Fixing capitalization

Bell: 1 revision

2014-06-09T14:21:52Z

1 revision

Andwar: minor typo correction (want't --> don't feel like); linked the 'Plugin manager' page

2014-06-06T10:19:53Z

minor typo correction (want't --> don't feel like); linked the 'Plugin manager' page

Bell: 14 revisions

2014-03-28T03:06:30Z

14 revisions

Pyadmin: 1 revision

2014-03-28T02:16:15Z

1 revision

Folf: /* For Linux users */ changed the output path (deleted /Software/pymol)

2012-08-13T11:28:01Z

For Linux users: changed the output path (deleted /Software/pymol)

Jaredsampson: /* Adding Pymol-script-repo to PyMOL search path */ clarified date of rev 3997

2012-07-06T16:35:54Z

Adding Pymol-script-repo to PyMOL search path: clarified date of rev 3997

@@ Line 7: / Line 7: @@
   /home/YOURNAME/Pymol-script-repo
-Now go to: '''Adding Pymol-script-repo to PyMOL search path''' [http://www.pymolwiki.org/index.php/Git_install#Adding_Pymol-script-repo_to_PyMOL_search_path]
+Continue with [[#Adding Pymol-script-repo to PyMOL search path]]
 == Git install instructions ==
@@ Line 41: / Line 41: @@
 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:
@@ Line 50: / Line 48: @@
 # Add paths to sys.path so PyMOL can find modules and scripts
 import sys, os
-pymol_git = os.path.abspath(os.path.join(os.path.expanduser('~'), 'Pymol-script-repo'))
+pymol_script_repo = os.path.abspath(os.path.join(os.path.expanduser('~'), 'Pymol-script-repo'))
-os.environ['PYMOL_GIT_MOD'] = os.path.join(pymol_git,'modules')
+pymol_script_repo_plugins = os.path.join(pymol_script_repo, "plugins")
-sys.path.append(pymol_git)
+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)
-# Make starting directory and change to it.
+os.environ['PYMOL_GIT_MOD'] = pymol_script_repo_modules
 </syntaxhighlight>
@@ Line 67: / Line 62: @@
 === 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:
- import os
- print os.environ['PYMOL_PATH']
+<syntaxhighlight lang="python">
 In this folder, you place "run_on_startup.py" and the Pymol-script-repo directory.<br>
 Write in "run_on_startup.py" :
@@ Line 78: / Line 76: @@
 # Add paths to sys.path so PyMOL can find modules and scripts
 import sys, os
-pymol_git = os.path.abspath(os.path.join(os.environ['PYMOL_PATH'], 'Pymol-script-repo'))
+pymol_script_repo = os.path.abspath(os.path.join(os.environ['PYMOL_PATH'], 'Pymol-script-repo'))
-os.environ['PYMOL_GIT_MOD'] = os.path.join(pymol_git,'modules')
+pymol_script_repo_plugins = os.path.join(pymol_script_repo, "plugins")
-sys.path.append(pymol_git)
+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)
-# Make starting directory and change to it.
+os.environ['PYMOL_GIT_MOD'] = pymol_script_repo_modules
 # Make setting changes to Plugin Manager
 import pymol.plugins
-pymol.plugins.preferences = {'instantsave': False, 'verbose': False}
+pymol.plugins.autoload['apbs_tools'] = False
-pymol.plugins.autoload = {'apbs_tools': False}
+pymol.plugins.preferences['verbose'] = False
-pymol.plugins.set_startup_path([os.path.join(pymol_git, 'plugins'), os.path.join(sys.prefix, 'Lib', 'site-packages', 'pmg_tk', 'startup')])
+_plugin_search_path = pymol.plugins.get_startup_path()
-pymol.plugins.preferences = {'instantsave': True, 'verbose': False}
+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.
- print sys.path
- import colorbydisplacement
+<syntaxhighlight lang="python">
- help(colorbydisplacement)
+print(sys.path)
 == Get latest changes to scripts ==
@@ Line 117: / Line 115: @@
 = Do you want to contribute with a script? =
 Information how to contribute scripts to the repository. It's easy! <br>
-http://www.pymolwiki.org/index.php/git_authors
+[git authors]

@@ Line 67: / Line 67: @@
 === Making a general "run_on_startup.py" - for all users ===
-This section describes automatic loading of plugins using PyMOL's [[Plugin manager]], which is available in newer PyMOL versions (e.g. 1.7, or higher).<br>
+This section describes automatic loading of plugins using PyMOL's [[Plugin Manager]], which is available in newer PyMOL versions (e.g. 1.7, or higher).<br>
 If you have a shared PyMOL installation for several linux computers, you can make general wide changes for the startup of PyMOL.<br>

@@ Line 1: / Line 1: @@
 == Manual download of scripts ==
-If you don't have the option or want't to install git on your system, then go to
+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.
@@ Line 67: / Line 67: @@
 === 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:

@@ Line 36: / Line 36: @@
   cd /home/YOURNAME/
   git clone git://github.com/Pymol-Scripts/Pymol-script-repo.git
-You now have all the scripts available in: /home/YOURNAME/Software/pymol/Pymol-script-repo
+You now have all the scripts available in: /home/YOURNAME/Pymol-script-repo
 == Adding Pymol-script-repo to PyMOL search path ==

@@ Line 41: / Line 41: @@
 You now have to add the "Pymol-script-repo" directory to the PyMOL search path.
-PyMOL has since revision 3997 (30/04/21012) an improved plugin/script manager.
+PyMOL has since revision 3997 (30 April 2012) an improved plugin/script manager.
 You have to remove old installations of plugins first, to get the automatic plugin installation to work.
 === Making a personal "pymolrc" file - for personal use ===

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