Hi Gianluigi, PyMOL might find more pymolrc files than you are aware of. Just to be sure, try this to get a hint:
PyMOL> print invocation.options.deferred Also, check which plugins are installed and eventually disable them. Cheers, Thomas Gianluigi Caltabiano wrote, On 07/23/13 10:44: > Hi Thomas, > > thank you for answering so fast. > > I do not have set retain_order, 1 in my pymolrc, but you are right, if I > set retain_order, 0 the problem disappears. It is strange because I do > not generally use retain_order, but still I might have used it and for > some reason it have been kept by pymol. > > cheers, > > Gianluigi > > ------------------------------------------------------------------------ > Da: Thomas Holder <thomas.hol...@schrodinger.com> > A: Gianluigi Caltabiano <chimic...@yahoo.it> > Cc: pymol-users <pymol-users@lists.sourceforge.net> > Inviato: Martedì 23 Luglio 2013 9:27 > Oggetto: Re: Residue numeration problem > > Hi Gianluigi, > > I can only reproduce your problem with retain_order=1, not with > retain_order=0 (which is the default). Could it be that in your pymolrc, > you do "set retain_order, 1"? > > I don't think there is a difference between 1.6 and previous versions. > > Cheers, > Thomas > > Gianluigi Caltabiano wrote, On 07/23/13 09:48: >> Hi all, >> >> Since 1.6.0.0 on my Mac (OSX 10.8.4) I am experiencing an annoying >> behaviour both when creating a new object from two existing and when >> mutating a residue via mutagenesis wizard (both with Macpymol and X11) >> >> Creating a new object from two existing, mess up the two (different) > chains. >> set retain_order, 1 does not change this behaviour. >> >> As for the new object creating try to reproduce this: >> >> fetch 4DAJ >> create MA, 4DAJ and chain A >> create MB, MA >> alter MB, chain='B' >> create dim, MA MB >> >> >> The new object is not ordered on a chain basis, but on residue number. >> >> Something very similar happens using mutagenesis wizard, in that case it >> mess the new residue with the first residue. In this cases closing PyMol >> and reopening (or chainging to Hybrid) often, but not always, works. >> Still is a pain in the back. >> >> Any clues? >> >> cheers, >> >> Gianluigi -- Thomas Holder PyMOL Developer Schrödinger Contractor ------------------------------------------------------------------------------ See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
