[gmx-users] find the relevant structure out

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Nov 24 06:27:01 CET 2010


> 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@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,


>> 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
> 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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