[gmx-users] find the relevant structure out

[Mark Abraham]

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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