Quoting #ZHAO LINA# <zhao0...@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-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf > of Mark Abraham [mark.abra...@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 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 ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
