Re: [PyMOL] How to export secondary structure information from a PDB using PyMol?

[Tsjerk W. <ts...@gm...>]

Hi Zhang Cheng,

If you replace SELECTION with a proper selection statement (with quotes),
then something like:

open("ss.dat","w").writelines( ["Residue %d: %s\n"%(a.resi,a.ss) for a in
cmd.get_model(SELECTION+" and n. ca").atom] )

It will write the results to a file called ss.dat. Do mind all
parentheses/brackets.

Hope it helps,

Tsjerk

On Fri, May 13, 2016 at 10:30 PM, ZHANG Cheng <272...@qq...> wrote:

> Dear PyMol friends,
> I would like to export the secondary structure of individual residues from
> a PDB. Can I ask if I can use PyMol to do that?
>
> I would like something like this:
>
> Residue 1: alpha-helix
> Residue 2: beta-sheet
> ......
>
>
>
> I think "http://webclu.bio.wzw.tum.de/cgi-bin/stride/stridecgi.py" can
> also do that. However, I found that one residue is loop in Pymol but is
> indicated as "strand" in the website. So I wonder if Pymol can output the secondary
> structure of individual residues from a PDB?
>
> Thank you.
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.