Protein 3D Structure Principal Axes

Question

[Woa]

Can anyone suggest some free software for calculating the principal axes for a protein 3d structure? Ideally the input will be the PDB file of 3d coordinates, and the program will return the moment of inertia tensor and the principal axes. I DON'T want the molecule to orient further along the principal axes.

There are a few examples of codes available in the net, but it would be good if someone knows about a well known software to do this job.

Thanks in advance

Answer 1

[Keith Callenberg]

Here are several options:

• Paul Grayson wrote a Tcl/Tk-based orient script you can use in VMD. It will calculate the principal axes. For you, just skip the 'move' command. http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/orient/

• I rewrote the above code in Java. It needs the Colt package for some of the linear algebra functions. http://mem.bio.pitt.edu/?q=node/89

• The MODELLER software package has a built-in orient command that is very fast: http://salilab.org/modeller/9v4/manual/node180.html For you, if you don't want to actually orient it, just skip the mdl.write() line and use the r.translation() data. Note that since MODELLER is written for homology stuff this will ignore hydrogens by default. To keep your hydrogens you'll want to add this line right after the env = environ() line:

  env.io.hydrogen = True

[Woa]

great!!! many thanks

Answer 2

[Pierre Poulain]

Dear Chris,

Albeit not being a "well known" software, I have a Python script that nicely does the job. In addition, it produces a .pml script for a rendering with the Pymol molecular viewer. I am not (yet) used to github so I posted the script here http://pastebin.com/m8wryusp

I hope it helps.

Cheers

Pierre

[Pierre Lindenbaum]

and welcome on Biostar @pierrepo ;-)

[Woa]

Thanks for the code

Answer 3

[Dejian]

Can DeepView (Swiss Pdb-Viewer) do this job?