[gmx-users] find the relevant structure out

Justin A. Lemkul jalemkul at vt.edu
Tue Nov 23 17:55:44 CET 2010

Quoting #ZHAO LINA# <ZHAO0139 at e.ntu.edu.sg>:

> I really do not know how to get those beta-sheet structures out,
> or maybe by which ways?

Visualization software can sometimes assign the secondary structure incorrectly.
 If you have some justifiable reason to believe that a certain secondary
structure exists (i.e. DSSP, STRIDE, etc) then you can use the "alter" feature
of PyMOL to render the secondary structure in the way that you believe to be


> Any clues are warmly welcomed and appreciated.
> lina
> ________________________________
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf
> of Mark Abraham [Mark.Abraham at anu.edu.au]
> Sent: Sunday, November 21, 2010 11:58 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] find the relevant structure out
> On 21/11/2010 11:43 PM, #ZHAO LINA# wrote:
> Hi,
> I had done 10ns simulation,
> by dssp, can see the beta-sheet appeared very apparently, before it's
> alpha-helix.
> there were 5000 frames, I based on the time of the picture got from dssp, I
> can guess around which frames is supposed to have those beta sheets.
> After I took few frames which I thought might be representive, but under
> pymol, show cartoon, there is none beta sheet at all. There were 5000 frames,
> I really do not know which one is most representive.
> Or maybe some parts I understand wrong.
> Thanks for any advice and if I am wrong please let me know,
> We've really no idea of the detail of what you've done, so can't guess. Just
> about anything could be the problem - all the way from "you are looking at
> the wrong files", to "pymol's definition of a beta sheet doesn't agree with
> dssp".
> If you can't report the command lines you used easily, then your method was
> not reproducible enough, or not recorded well enough :-)
> Mark


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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