[gmx-users] find the relevant structure out

[#ZHAO LINA#]

I do not know how to extract some special frames out (professionally),
so I just simply use vim to take the relevant models out and put into a new pdb file.
Are there some good ways to extract one or two frames at the end of those whole frames?

Base on your answering, now I start to suspect I might make something wrong cause I did it really clumsily.

Thanks for your answering,

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: Wednesday, November 24, 2010 3:19 PM
To: Discussion list for GROMACS users
Subject: Re: RE: [gmx-users] find the relevant structure out



----- Original Message -----
From: #ZHAO LINA# <ZHAO0139 at e.ntu.edu.sg>
Date: Wednesday, November 24, 2010 17:52
Subject: RE: [gmx-users] find the relevant structure out
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

> Hi,
>
> Thanks for your answering.
>
> Due to the difference in assignment, so I wonder which one I
> should build a bit much more faith on?
>
> I read (by eyes) the ss.xpm produced by do_dssp, and find the
> relevant resi out which showed as beta-sheet, but in pymol, it's
> really so standard alpha-helix, when I tried "alter" in pymol to
> show the beat-sheet as the way Justine mentioned in early email,
> it's really look weird.


It's rather more likely that you're comparing two different (parts of) structures, than one secondary structure algorithm assigns sheet and one assigns helix to the same part of the same structure. Is the residue/atom numbering consistent. What does do_dssp say about the frame you cut out to give to pymol?


Mark

>
> I noticed lots of paper they use DSSP to say something.
>
> Thanks,
>
> lina
> ________________________________________
> From: gmx-users-bounces at gromacs.org [gmx-users-
> bounces at gromacs.org] on behalf of Tsjerk Wassenaar [tsjerkw at gmail.com]
> Sent: Wednesday, November 24, 2010 1:27 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] find the relevant structure out
>
> Hi,
>
> > Visualization software can sometimes assign the secondary
> structure incorrectly.
>
> There has been an interesting discussion on this on the Pymol user
> list years ago (http://www.mail-archive.com/pymol-
> users at lists.sourceforge.net/msg01574.html).Secondary structure
> assignment is foremost human defined. You can use
> different metrics to obtain assignments, and should be careful
> to take
> any one of them as 'correct'. For instance, it makes a difference
> whether you assign three types (helical, sheet, loop), as Pymol does,
> or like seven types, as DSSP does.
>
> In pymol you can set the secondary structure type manually, but
> I find
> that the internal command 'dss' usually does a good job. Note
> that it
> only works on one frame and then uses the assignment for that
> frame on
> all of them, although there may be a workaround (I'll check; something
> with discrete_states). The frame to use for the assignment can be
> given to the 'dss' command through the argument state=N, where N is
> the frame number. If dss doesn't give the assignment you want,
> you can
> also try 'util.ss' that uses a different metric.
>
> Hope it helps,
>
> Tsjerk
>
> >> 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
> >
> > ========================================
> > --
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
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