Pymol2glmol

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Revision as of 20:50, 16 January 2012 by Tlinnet (Talk | contribs)
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Type Python Script
Download pymol2glmol.py
Author(s) Takanori Nakane
License LGPL3
This code has been put under version control in the project Pymol-script-repo

Contents

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.

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,
Takanori Nakane

Example of use

reinitialize
import pymol2glmol
 
fetch 1TQN, async=0
preset.pretty_solv("1TQN")
select heme, organic
 
pymol2glmol 1TQN
import webbrowser
webbrowser.open("1TQN.html")

System requirements

GLmol runs on newer versions of Firefox, Chrome, Safari or Opera.
Internet Explorer is not supported because IE doesn't implement WebGL.

GLmol also runs on Sony Ericsson's Android devices which support WebGL.
Support for Firefox Mobile is currently underway.
Reportedly, GLmol also runs on WebGL enabled safari in iOS.

If you see only black screen and you are using

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

Install menu editor, and run it

sudo apt-get install alacarte
sudo alacarte

Locate internet menu. Edit the "Google Chrome" entry from->to

/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.
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

Then locate the line Exec= and insert in line --enable-webgl:

Exec=/opt/google/chrome/google-chrome --enable-webgl %U
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