Thanks a lot Warren. If you allow me, my script to build sequences of 3 peptides is almost done. I could even use sculpt to improve my molecules structures.
For the moment I am missing just one thing. I want to make the N-term and C-term (NH3+ and COO-) automatically for all 20 tripeptide. I know how to to do it by mouse, but how to 'add hydrogens' and 'make pk1 positive', e. g., by command? Thanks a lot for PyMol. Cheers, Alan On 20/03/06, Warren DeLano <war...@delsci.com> wrote: > Alan, > > > Is PyMol able to save the built protein/molecule in a PDB > > file with CONECT information. If so, how to do it? > > Yes, > > set pdb_conect_all > > before saving the pdb file in order to get a PDB file with explicit > connectivity and valences for all atoms. > > Cheers, > Warren > > -- > Warren L. DeLano, Ph.D. > Principal Scientist > > . DeLano Scientific LLC > . 400 Oyster Point Blvd., Suite 213 > . South San Francisco, CA 94080 USA > . 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 Alan > > Sent: Monday, March 20, 2006 11:39 AM > > To: Pymol > > Subject: [PyMOL] Saving PDB with CONECT information > > > > Hello List! > > > > Is PyMol able to save the built protein/molecule in a PDB > > file with CONECT information. If so, how to do it? > > > > Thanks in advance for any help. > > > > Cheers, > > Alan > > -- > > Alan Wilter S. da Silva, D.Sc. - Research Associate > > Department of Biochemistry, University of Cambridge. > > 80 Tennis Court Road, Cambridge CB2 1GA, UK. > > > > > > ------------------------------------------------------- > > This SF.Net email is sponsored by xPML, a groundbreaking > > scripting language that extends applications into web and > > mobile media. Attend the live webcast and join the prime > > developer group breaking into this new coding territory! > > http://sel.as-us.falkag.net/sel?cmd=k&kid0944&bid$1720&dat1642 > > _______________________________________________ > > PyMOL-users mailing list > > PyMOL-users@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > > > > -- Alan Wilter S. da Silva, D.Sc. - Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK.
