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";<tsje...@gmail.com>;
Date: Sat, May 14, 2016 07:49 PM
To: "ZHANG Cheng"<272699...@qq.com>;
Cc: "pymol-users"<pymol-users@lists.sourceforge.net>;
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" <272699...@qq.com> 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";<tsje...@gmail.com>;
Date: Sat, May 14, 2016 05:24 AM
To: "ZHANG Cheng"<272699...@qq.com>;
Cc: "pymol-users"<pymol-users@lists.sourceforge.net>;
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 <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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