[Chimera-users] Ligand Problem

[Elaine Meng]

Hi Marcus,
Thanks for being a fan!

The automatic categorization is convenient in many ways, but for specific cases such as yours where it doesn't get what you want, you can still accomplish your ultimate goals, depending what they are.

If you want the surface to envelop the ligand with the microglobulin domains instead of considering it separately, you can create your own surface category with command surfcat. I don't know the details of the PDB you are using so I can't give the specific command for your situation.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/msms.html>

If it isn't a surface issue, just convenience with commands, you can use either named selections or the alias command to give any set of atoms a name that can be used to specify them in other commands, or the word "protein" may work in your case to specify both the protein and the peptide ligand:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/namesel.html>

I hope this helps… if not, maybe say which PDB ID you are using (if publicly available) and/or more about why you don't want the peptide classified as ligand.  Best,
Elaine
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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 14, 2014, at 11:13 AM, "Marcus Fabiano A. Mendes" <cla_atm_milo at hotmail.com> wrote:

> Hi,
> My Name is Marcus, and I am a huge fan of Chimera. Currently, I'm using Chimera to visualize p:MHC complex and it's electrostatic potential map. p:MHC occurs as an α chain composed of three domains - α1, α2, α3, β2 microglobulin and a ligand present in the groove. Chimera automatically recognizes the epitope as a ligand, since they have on average less than 10 amino acids. There's someway to make the Chimera don't recognizes this epitope as a ligand? A option to set the parameters that Chimera uses (ligand = <10 amino acids)?
> Thanks for All
> Sincerely
> Marcus Mendes