Hi, The wiki has a page on this:
http://www.pymolwiki.org/index.php/Peptide_Sequence except it doesn't mention the zwitterion details. There's a link to Robert Campbell's scripts to do this sort of thing, so maybe the answer is there. As for for loops, this is best in a full python script (run with "run"). In fact, your pseudocode is almost valid python. More like: residues = ("A", "C", "D", "E", "F", "G", "H" etc) for residue in residues: for i in range(3): cmd._alt(residue.lower()) cmd.set_geometry ?? cmd.save(aa.pdb, "all") Unfortunately, I'm not sure the set_geometry command is right. gilleain torrance On 3/14/06, Alan <alanwil...@gmail.com> wrote: > Hello List, > > I would like to have any help. > > I want to build several 3-peptides, like AAA, FFF, KKK etc. I also > would like to make them zwitterionics, add chain and save as a PDB > file. > > I know how to do that using the graphic interface, but I what I am > looking for is a way to do it via pymol script. > > Is is possible? May anyone give a idea of how create the 3-peptides > and put right N- and C- terminals? > > BTW, a loop with "for" is possible in pymol scripting? > > Summarising, I am trying a script like this: > > ----------------------- > residue = ( ALA, ARG, etc) > > for res in residue: > 'create peptide res-res-res' > 'set NH3 in res 1 and COO- in res 3' > > save aa.pdb, all > ----------------------- > > Thanks a lot 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?cmdlnk&kid0944&bid$1720&dat1642 > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
