Torsion angle calculations for multi-model PDB file

[Former user]

I want to calculate all torsion angles for a multi-model PDB file. When I ran torsion.pdb, I am able to see the angles only for one model. How to get angles for all the models?

[Xinqiu Yao]

Hi,

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As far as I know, torsion.pdb()only takes the first model. A solution is to use the xyz2torsion.R (and the associated documentation, xyz2torsion.Rd) under new_funs/ here. The function hasn’t been integrated into the bio3d package. So, to use it, you need to source() first.

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Let me know if you get any problems.

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[Ashraya Ravikumar]

Thanks for this! I ran the script but in the output, I only see phi, psi and chi1 even for longer side chain residues. How do I get chi2,chi3, etc. ?

[Xinqiu Yao]

You can use the tbl argument to set the angles (e.g., “chi1” up to “chi5”). See xyz2torsion.Rd for more detail.

[Ashraya Ravikumar]

Thanks a lot for pointing this out. Is there some way to output omega angle as well? Even when I mention ‘all’, it does not calculate omega angle.

[Xinqiu Yao]

No, it doesn’t output omega. One solution may be to split the multi-model file into multiple PDB files and then repeatedly use torsion.pdb() to get omega.

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