VMD-L Mailing List

From: Daniel Gaston (daniel.gaston_at_DAL.CA)
Date: Tue Apr 21 2009 - 12:01:08 CDT

Excellent, I had come across the script earlier but thought that I would
have been limited to overriding the whole structure instead of just
selected residues. This is excellent to know, thank you very much.

Dan

John Stone wrote:
> Hi,
> Have a look at this script, you should be able to
> use a similar strategy to override parts of the secondary structure
> prediction from STRIDE with whatever other information you
> have from other sources:
> http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/vmd_use_pdb_ss/
>
> The key VMD command of interest in the script is:
> $sel set structure $ss
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Apr 21, 2009 at 11:25:08AM -0300, Daniel Gaston wrote:
>
>> Hi all,
>>
>> I am wondering if there is a method to override STRIDE's secondary
>> structure prediction (and thus how VMD displays it in New Cartoon
>> format) for only a specified portion of a structure file? I have a
>> Homology Model from Swissprot where one loop region in only one chain of
>> a homodimer is show as as anti-parallel beta-sheet instead of the loop
>> region that it should be. Because only this one portion is incorrect
>> (and because Swissprot homology models contain only coordinates and not
>> a secondary structure section) I would like to override the
>> representation only for that one area of the structure without needing
>> to create a secondary structure entry in the PDB for the entire protein.
>> Is this possible?
>>
>> Thank you,
>>
>> Dan Gaston
>>
>> --
>> Daniel Gaston
>> PhD Candidate, Dr. Andrew Roger Lab
>> Department of Biochemistry and Molecular Biology
>> Dalhousie University, Nova Scotia, Canada
>>
>
> 

-- 
Daniel Gaston
PhD Candidate, Dr. Andrew Roger Lab
Department of Biochemistry and Molecular Biology
Dalhousie University, Nova Scotia, Canada