[Chimera-users] Ligand Problem

Marcus Fabiano A. Mendes cla_atm_milo at hotmail.com
Fri Aug 15 11:33:21 PDT 2014

First of all, thanks for the answers. You have a great software and a great support. The Eric's solution was exactly what I was looking for, and worked perfectly. 
Many Thanks againMarcus Mendes
Subject: Re: [Chimera-users] Ligand Problem
From: pett at cgl.ucsf.edu
Date: Thu, 14 Aug 2014 11:47:48 -0700
CC: chimera-users at cgl.ucsf.edu
To: cla_atm_milo at hotmail.com

Hi Marcus,	There is no preference or control for this in the normal Chimera interface, but all things are possible in Python.  The line of Python code that checks that ligands are less than 10 residues is line 169 in <your Chimera>/share/Categorizer/__init__.py .  Change the '10' in that line to whatever value works for you and save the file.  Subsequent uses of Chimera will use the lower value.	If you are using a Mac, then "<your Chimera>" is Chimera.app/Contents/Resources.  You will have to right click on Chimera.app in the Finder and choose "Show Package Contents" to get to the folders inside Chimera.app.
                        Eric Pettersen
                        UCSF Computer Graphics Lab

P.S.  All of Elaine's suggestions are also good approaches.
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
SincerelyMarcus Mendes_______________________________________________
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