[gmx-users] find the relevant structure out

[#ZHAO LINA#]

do_dssp -f traj.xtc -s topol.tpr -o ss.xpm

trjconv -s topol.tpr -f traj.xtc -o protein.pdb -pbc nojump

Took several frames, here, such as model 1000, model 3000 and model 5000, and named as 1000.pbd, 3000.pdb and 5000.pdb

pymol 3000.pdb

intra_fit protein and (name c,n,ca)

show cartoon

all the way from "you are looking at the wrong files", to "pymol's definition of a beta sheet doesn't agree with dssp".

what are those files I should have looked for, and how could I find a better way to show those beta-sheet out?

Thanks,

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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