My software notes

June 28, 2012

[PyMOL] Draw Goodsell-like view using GLSL

Filed under: pymol/ molmol — kpwu @ 12:10 am
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There is a new post in Pymol user mailing list showing an approach to draw the “Goodsell-like” molecule. The most famous Goodsell molecular images are the “Molecule of the month” at PDB-101. Dr. Goodsell also provides online version of images used in his book: “The Machinery of Life“.

That detail of Goodsell-like presentation in pymol is available at PyMOLWiki. It mainly uses GLSL rendering technique. I practiced several times and found out that my MacPyMOL version (2 years old) is not able to run such rendering (OpenGL only..). Therefore I used macports to install PyMOL 1.5 (run under X11).

There may be a wrong description at PyMOLWiki — I rename the “sphere.fs” to “sphere.fs.bak” and copy and save the author’s code (at PyMOLWiki) as “sphere.fs” (not shaders.fs).

Here is another 2 tries I have done using PDB files 2Y1M and 2WCC for top 2 figures and the bottom DNA figure, respectively.

June 26, 2012

[PyMOL] contact map (CMView)

Filed under: pymol/ molmol,softwares and scripts — kpwu @ 1:59 am
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In PyMOL Wiki, there is a “contact map visualizer” plugin providing users to inspect the protein intramolecular contacts. However, this plugin requires “PyGame”, “Tkinter”, “PIL (python image library)” and most importantly, Gromacs!

I used Fink (Mac OSX 10.6.8) to successfully install Gromacs 4.1 but Fink reported problems while installing pygame. So I can generate xpm file of target protein structure by Gromacs but not inspect the contact map in PyMOL.

In contrast, I found another contact map visualizer called “CMView – Protein contact map visualization and analysis“. This program is written in Java and uses PyMOL as the molecular viewer.

Installation note (work platform: Mac OSX 10.6.8 with X11)

1. Download the CMView file, unzip it and move the folder to proper path)

2.Edit the “cmview.cfg” file and correct the path of pymol execute. Optional programs such as DSSP and DALI can be used if installed.

3. In terminal, call “” and load the PDB file from “CMView” and enjoy visualizing the molecules.

While the PDB is loaded, the CMView (run in Java) will show you the contact map.  You can use mouse to crop the region of interest and instantly see the contacts in the PDB file.

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