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

[Tsjerk Wassenaar]

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 <272699...@qq.com> 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.
--
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[PyMOL] How to export secondary structure information from a PDB using PyMol?

[ZHANG Cheng]

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.--
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net