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

[Z. C. <272...@qq...>]

Hi Julian,
Thank you so much. I just tested it and it worked as well!


Yours sincerely
Cheng




------------------ Original ------------------
From:  "Julian Heinrich";<ju...@jo...>;
Date:  Wed, May 18, 2016 01:37 AM
To:  "ZHANG Cheng"<272...@qq...>; "pymol-users"<pym...@li...>; 

Subject:  Re: [PyMOL] How to export secondary structure information from a PDBusing PyMol?



Hi,

in case you haven't solved this yet, the following command prints the residue number and secondary structure:


iterate n. CA, print resi + ':' + ss



Cheers,
Julian


On Fri, May 13, 2016 at 10:40 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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