Pymol2glmol - Revision history

Bell: 9 revisions

2014-03-28T03:36:36Z

9 revisions

Tlinnet: /* System requirements */

2012-01-16T21:31:32Z

System requirements

Tlinnet: /* Fix explained for Mint 12, gnome shell 3, chrome 16 */

2012-01-16T21:15:38Z

Fix explained for Mint 12, gnome shell 3, chrome 16

Tlinnet at 21:02, 16 January 2012

2012-01-16T21:02:56Z

Tlinnet: /* Fix explained for Mint 12, gnome shell 3, chrome 16 */

2012-01-16T20:50:18Z

Fix explained for Mint 12, gnome shell 3, chrome 16

Tlinnet: /* Fix explained for Mint 12, gnome shell 3, chrome 16 */

2012-01-16T20:45:02Z

Fix explained for Mint 12, gnome shell 3, chrome 16

Tlinnet at 20:30, 16 January 2012

2012-01-16T20:30:28Z

Tlinnet at 20:17, 16 January 2012

2012-01-16T20:17:47Z

Tlinnet: /* Example of use */

2012-01-16T20:10:16Z

Example of use

Tlinnet: Created page with "{{Infobox script-repo |type = script |filename = pymol2glmol.py |author = Takanori Nakane |license = - }} == Introduction == A script to export a scene in pymol to GLm..."

2012-01-16T20:06:11Z

Created page with "{{Infobox script-repo |type = script |filename = pymol2glmol.py |author = Takanori Nakane |license = - }} == Introduction == A script to export a scene in pymol to GLm..."

New page

{{Infobox script-repo
|type = script
|filename = pymol2glmol.py
|author = Takanori Nakane
|license = -
}}
== Introduction ==
A script to export a scene in pymol to GLmol. GLmol is a molecular viewer for Web browsers written in WebGL/Javascript.

With '''pymol2glmol''', you can publish your pymol scene to a Web page. Visitors can rotate, zoom the molecule on the page.

Compared to export of polygon coordinates (VRML or Object3D), the published web page contain only atomic coordinates so that
the file size is much smaller and visitors can even change representation.

[http://webglmol.sourceforge.jp/pymol_exporter/index.html Examples and script can be downloaded from my web page.]

This script uses '''cmd.get_session''' to extract which representations is enabled on each part of the molecule.
I think this technique is useful for many purposes, for example, writing exporters, copying representations between aligned structures, etc.

Comments and suggestions are welcome.

Best regards, <br>
Takanori Nakane

== Example of use ==
<syntaxhighlight lang="python">
reinitialize
import pymol2glmol

fetch 1TQN, async=0
preset.pretty_solv("1TQN")
select heme, organic

pymol2glmol 1TQN
</syntaxhighlight>

[[Category:Script_Library]]
[[Category:ThirdParty_Scripts]]
[[Category:Pymol-script-repo]]

← Older revision		Revision as of 21:31, 16 January 2012
Line 42:		Line 42:

	GLmol runs on newer versions of Firefox, Chrome, Safari or Opera. <br>		GLmol runs on newer versions of Firefox, Chrome, Safari or Opera. <br>
		+	[http://www.windows7hacker.com/index.php/2010/02/how-to-enable-webgl-in-firefox-chrome-and-safari/ See here how to activate in windows.]
	Internet Explorer is not supported because IE doesn't implement WebGL.		Internet Explorer is not supported because IE doesn't implement WebGL.

@@ Line 65: / Line 65: @@
 If you use the repository version of chrome, then search for '''chromium-browser.desktop''' instead.
   less ~/.local/share/applications/mimeapps.list | grep 'text/html'
-  sudo find / -name 'google-chrome.desktop' | xargs gedit
+  sudo find / -name 'google-chrome.desktop' | xargs sudo gedit
 Then locate the line '''Exec=''' and insert in line '''--enable-webgl''':
   Exec=/opt/google/chrome/google-chrome --enable-webgl %U

@@ Line 60: / Line 60: @@
   /opt/google/chrome/google-chrome %U
   /opt/google/chrome/google-chrome --enable-webgl %U
-Then find out what handles your default opening of '''text/html''', and edit that .desktop file.
+Then find out what handles your default opening of '''text/html''', and edit that .desktop file.<br>
   less ~/.local/share/applications/mimeapps.list | grep 'text/html'
   sudo find / -name 'google-chrome.desktop' | xargs gedit

@@ Line 60: / Line 60: @@
   /opt/google/chrome/google-chrome %U
   /opt/google/chrome/google-chrome --enable-webgl %U
-Then find out what handles your '''text/html''', and edit that .desktop file.
+Then find out what handles your default opening of '''text/html''', and edit that .desktop file.
-  less ~/.local/share/applications/mimeapps.list
+  less ~/.local/share/applications/mimeapps.list | grep 'text/html'
+  sudo find / -name 'google-chrome.desktop' | xargs gedit
+Then locate the line '''Exec=''' and insert in line '''--enable-webgl''':
 [[Category:Script_Library]]
 [[Category:ThirdParty_Scripts]]
 [[Category:Pymol-script-repo]]

← Older revision		Revision as of 20:10, 16 January 2012
Line 33:		Line 33:

	pymol2glmol 1TQN		pymol2glmol 1TQN
		+	import webbrowser
		+	webbrowser.open("1TQN.html")
		+
	</syntaxhighlight>		</syntaxhighlight>

← Older revision	Revision as of 03:36, 28 March 2014
(No difference)

@@ Line 22: / Line 22: @@
 Best regards, <br>
 Takanori Nakane
 == Example of use ==

@@ Line 35: / Line 35: @@
 import webbrowser
 webbrowser.open("1TQN.html")
-</syntaxhighlight>
+GLmol also runs on Sony Ericsson's Android devices which support WebGL. <br>
 [[Category:Script_Library]]
 [[Category:ThirdParty_Scripts]]
 [[Category:Pymol-script-repo]]

@@ Line 3: / Line 3: @@
 |filename  = pymol2glmol.py
 |author    = Takanori Nakane
-|license   = -
+|license   = [http://opensource.org/licenses/LGPL-3.0 LGPL3]
 }}
 == Introduction ==