[gmx-users] find the relevant structure out

[Justin A. Lemkul]

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
correct.

-Justin

> 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
>


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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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