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

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu

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@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 á chain composed of three domains - á1, á2, á3, â2 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
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