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
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 ---------- 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@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
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 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 _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi 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@cgl.ucsf.edu Date: Thu, 14 Aug 2014 11:47:48 -0700 CC: chimera-users@cgl.ucsf.edu To: cla_atm_milo@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 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 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_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
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Elaine Meng -
Eric Pettersen -
Marcus Fabiano A. Mendes