VMD-L Mailing List

From: Daniel Gaston (daniel.gaston_at_DAL.CA)
Date: Tue Apr 21 2009 - 10:29:03 CDT

Thank you for the reply,

In regards to option b, I should have mentioned that I have already
subjected these structures to minimzation and and MD tun (1.5 ns or so
worth). The beta sheet predicted structure in that case has been reduced
but not eliminated entirely, at least when done in a water sphere. I
believe when I minimize and do the MD in a vacuum (done initially by
mistake) that it was resolved.

Option A does work. Ideally I would like to break and resolve that loop
altogether. Oddly enough this is a case where I submit the same
alignment to Swiss-Model using the same template structure (a homodimer)
and only change which Chain is used as the template (A versus B). The A
chain model works perfectly, it is only on the B chain that this loop
appears to be modeled incorrectly.

Thanks for the help. Any further suggestions/comments from users would
be appreciated.

Dan

L. Michel Espinoza-Fonseca wrote:
> Hi Daniel,
>
> There are two options I can think of:
>
> (a) You can use the 'new ribbons' rendering instead of the 'new
> cartoon' one. You can change the thickness of the ribbons to make it
> look like a cartoon but without worrying about the sheet depiction.
>
> (b) This option is more difficult, but better in terms of cleansing of
> incorrect geometries/contacts. Probably what you could do is to relax
> your protein using MD and minimize the final coordinates. This should
> give you an improved geometry. Remember that homology modeling often
> produces 'dirty' geometries. In this case STRIDE is just processing
> what you're giving to it, whether is correct or not.
>
> Cheers,
> Michel
>
> On Tue, Apr 21, 2009 at 4:25 PM, Daniel Gaston <daniel.gaston_at_dal.ca> 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