[Chimera-users] building a peptide

Elaine Meng meng at cgl.ucsf.edu
Wed Aug 28 09:11:29 PDT 2013


Hi Kumud,
I'm not sure whether you meant the peptide did not have the correct backbone angles, or that the ribbon doesn't look flat like the beta strand ribbons in proteins.

You can build peptides with specified phi and psi angles (including beta-strand values) using Build Structure, Start Structure tab, "peptide sequence" option:

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#start>

Maybe you did that part already and are instead concerned about the ribbon display. Even if the phi and psi angles are correct for a beta-strand, this does not mean the residue is automatically assigned as strand for ribbon display.  The reason it is not automatically assigned is because the method used (ksdssp) identifies strands only when they are H-bonded to other strands to form a sheet.  If the strand is by itself, it won't be automatically assigned.  However, you can assign it manually as strand for ribbon display if you want to. 

You can assign it manually by first selecting the residues you want to assign as strand, then using either:

(a) command setattr, for example: setattr r isStrand true sel

or
(b) the Selection Inspector (open by clicking the green magnifying glass on the right bottom corner of the Chimera window), inspect "Residue", and set "in strand" to "true" (and "in helix" should be "false")

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Aug 28, 2013, at 12:40 AM, Kumud Agarwal wrote:

> Hi
> I am very new to Chimera. I am using Chimera version 1.8.
> 
> I am trying to build a peptide in chimera in beta strand conformation
> using build structure option but the generated peptide did not show beta
> strand.
> Why is it so?
> 
> Thanks,
> Kumud Agarwal
> IIT Bombay
> India




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