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

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

Hi Zhang Chen,

Oh, I guess that the %d should be %s then. Sorry.

Cheers,

Tsjerk
On May 14, 2016 13:45, "ZHANG Cheng" <272...@qq...> wrote:

> Dear Dr Tsjerk,
> Thank you very much!.
>
> For example, I have a structure of "protein.pdb". I tried but seems not
> work:
>
> PyMOL>open("ss.dat","w").writelines(["Residue %d: %s\n"%(a.resi,a.ss) for
> a in cmd.get_model("protein"+" and n. ca").atom])
> Traceback (most recent call last):
>   File "D:\Program Files (x86)\PyMOL\PyMOL/modules\pymol\parser.py", line
> 464, in parse
>     exec(layer.com2+"\n",self.pymol_names,self.pymol_names)
>   File "<string>", line 1, in <module>
> TypeError: int argument required
>
> Can I ask how to modify that?
>
> Thank you!
>
>
> ------------------ Original ------------------
> *From: * "Tsjerk Wassenaar";<ts...@gm...>;
> *Date: * Sat, May 14, 2016 05:24 AM
> *To: * "ZHANG Cheng"<272...@qq...>;
> *Cc: * "pymol-users"<pym...@li...>;
> *Subject: * Re: [PyMOL] How to export secondary structure information
> from a PDBusing PyMol?
>
> 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.
>
>