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

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

Hi Zhang Chen,

Yes, Pymol only recognizes Helix (3-,alpha,pi), Sheet and Loop (including
turns and such).

Best,

Tsjerk
On May 14, 2016 13:55, "ZHANG Cheng" <272...@qq...> wrote:

> Dear Dr Tsjerk,
> Thank you very much. Now it works!
>
> There are only L, S, H
>
> So,
> L: loop
> S: beta-strand
> H: alpha-helix
>
> Is that right?
>
> Thank you.
>
> Cheng
>
>
> ------------------ Original ------------------
> *From: * "Tsjerk Wassenaar";<ts...@gm...>;
> *Date: * Sat, May 14, 2016 07:49 PM
> *To: * "ZHANG Cheng"<272...@qq...>;
> *Cc: * "pymol-users"<pym...@li...>;
> *Subject: * Re: [PyMOL] How to export secondary structure information
> from aPDBusing PyMol?
>
> 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.
>>
>>