[Chimera-users] Ribbon for a non-standard peptide

[Elaine Meng]

On Tuesday, February 1, 2005, at 12:14 AM, Jagannadh Dr B, Scientist  
wrote:

> Hi, I am new to Chimera
> Can any one suggest how one can draw a ribbon for a peptide which has
> non-standard residues
> Jagannadh

Hi Jagannadh,
If these nonstandard residues have the same backbone atoms
as regular amino acids (N, CA, C, O), it might work already,
although it depends on how these residues were specified in
the input file.  For example, many PDB files have the nonstandard
residue selenomethionine, MSE, but the ribbon is drawn just like
for the other residues (one such PDB file is 1kko).

However, it sounds like you already tried and did not get a ribbon
for these residues.  It must be that the backbone is different or
even that the backbone atoms have different names than N, CA, C, O.
You can use the "Residue Class" section of Ribbon Style Editor
(Tools... Graphics... Ribbon Style Editor) to define which atoms
determine the path of the ribbon for these nonstandard residues.

The instructions for creating a Residue Class can be viewed at:
http://www.cgl.ucsf.edu/chimera/1.2065/docs/ContributedSoftware/ 
ribbonstyle/ribbonstyle.html#class

Then, you could select the nonstandard residues and then Apply the
class you have created to those residues.  I can't really get more
specific without knowing more about these nonstandard residues, but
you can send me e-mail if you get stuck.
I hope this helps,
Elaine
----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html