[gmx-users] find the relevant structure out
Mark.Abraham at anu.edu.au
Sun Nov 21 16:58:36 CET 2010
On 21/11/2010 11:43 PM, #ZHAO LINA# wrote:
> I had done 10ns simulation,
> by dssp, can see the beta-sheet appeared very apparently, before it's
> 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
> 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 :-)
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