Ramon, Though PyMOL's molecular editor is extensible in this way, there are some pieces missing when it comes to adding new fragments into the mix. What you hope to do will require general design improvements followed by some Python development. For example, one of the problems with the peptide builder right now is that it it is relying on naming conventions that are valid for the limited subset of groups it knows, but wouldn't be in general.
Thus, it might make sense to use a tool other than PyMOL for the time being... Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > "Dr. Ramón Garduño-Juárez" > Sent: Tuesday, February 08, 2005 1:02 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Coordinates for End Groups > > Dear Pymol-users: > > We are working on an interface between PYMOL and ECEPP/3 > inorder to perform a conformational search in small peptides. > We have done most of the dirty work, but still can not figure > out how to include coordinates for End Groups other than the > ones given in the modules/chempy subdirectory. > > To make myself clear, I want to be able to build peptides > that would contain the following amino and carboxyl end groups: > AMINO-H2 > AMINO-H3+ > AMINO-CH3 > AMINO-COCH3 > FORMYL > CARBOXYL-COOH > CARBOXYL-O > CARBOXYL-CH3 > CARBOXYL-NHCH3 > METHYL-ESTER > ETHYL-ESTER > > Any help surely will be appreciated. Thank you all in advance. > > Cheers, >
