Question: Protein 3D Structure Principal Axes
1
gravatar for Woa
9.0 years ago by
Woa2.8k
United States
Woa2.8k wrote:

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

pdb protein • 5.8k views
ADD COMMENTlink modified 6.5 years ago by Biostar ♦♦ 20 • written 9.0 years ago by Woa2.8k
3
gravatar for Keith Callenberg
9.0 years ago by
Pittsburgh, PA
Keith Callenberg900 wrote:

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

ADD COMMENTlink written 9.0 years ago by Keith Callenberg900

great!!! many thanks

ADD REPLYlink written 9.0 years ago by Woa2.8k
3
gravatar for Pierre Poulain
9.0 years ago by
France
Pierre Poulain440 wrote:

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

ADD COMMENTlink written 9.0 years ago by Pierre Poulain440
1

and welcome on Biostar @pierrepo ;-)

ADD REPLYlink written 9.0 years ago by Pierre Lindenbaum127k

Thanks for the code

ADD REPLYlink written 9.0 years ago by Woa2.8k
1
gravatar for Dejian
9.0 years ago by
Dejian1.3k
United States
Dejian1.3k wrote:

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

ADD COMMENTlink written 9.0 years ago by Dejian1.3k
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