VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Tue Apr 21 2009 - 10:33:50 CDT

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
>
>