Hi all, I'd like to use the Mutagenesis wizard in a Pymol/Python script! I'd like to automate the following steps!
(1) Load a peptide pdb file with three residues. (easy) (2) Mutate one residue, well actually I do not want to change a single residue but change the rotamer of a residue. Unlike the mutagenesis wizard I'd like to use my own rotamer Library (It is based on Dunbrack's library but with slightly variations). So, I'd like to specify residue,phi,psi,chi1,chi2,chi3,chi4 for each rotamer I want to mutate to. (3) Save it in a pdb format (easy) I've found a magnificent start-up for my script from Andreas Henschel (see below). But I do not know how to load a specific rotamer (res,phi,psi,chi1,chi2,chi3 and chi4). Any ideas? All ideas are welcome, Josep Maria, PS: Well, a solution was done by the Rotamer Toggle (http://www.pymolwiki.org/index.php/Rotamer_Toggle), but this script is not working properly and out of date! --------------------------------------------- Josep Maria Campanera Alsina Juan de la Cierva Researcher Departament de Fisicoquímica Facultat de Farmàcia Avgda Joan XXIII, s/n 08028 Barcelona · Catalonia · Spain Tel: +34 93 4035988 Fax: +34 93 4035987 campan...@ub.edu -------------------------------------------- ---------------------------------------------------------------------------------------------------------------------- Hi Martin, you can get hints about how to script wizard functions if you log your activities while running the wizard. A python script (mutate.py) that makes use of the mutagenesis wizard could look like this: ## run through pymol, eg.: ## pymol -qc mutate.py 1god A/94/ ASN from pymol import cmd import sys pdb, selection, mutant = sys.argv[-3:] cmd.wizard("mutagenesis") cmd.fetch(pdb) cmd.refresh_wizard() cmd.get_wizard().do_select(selection) cmd.get_wizard().set_mode(mutant) cmd.get_wizard().apply() cmd.set_wizard() cmd.save("%s_m.pdb" % pdb, pdb) This is pretty no-frills, as no rotamer stuff is taken into account. I wrote it in Python, because it allows to parameterize from command line, you can add loops easily etc. Beware, the error message you get is because pymol unsuccessfully tries to open the command line arguments as files. Hope that helps. Best regards, Andreas Martin Höfling wrote: > Hi there, > > does anybody of you has an idea, if the mutagenesis stuff is available for use > inside scripts too? > > I wanna load a pdb, mutate a resid and save the resulting pdb via commandline. > > The only thing I found was modifying atoms, when I searched via "help" and > also checked the wiki, i hope that I didn't miss sth. > > Cheers > Martin
