Thanks Tsjerk (on both occasions). As a matter of fact, I'm kind of making a living out of writing a Python script once in a while, so thats no worry ;) What I was trying to get at was that I was trying to understand how certain PyMOL scripts work, and naturally from that become able to improve my own ones.
In particular, I was trying to understand the following script: http://pastebin.com/5mkwWJdd Its is supposed to find hydrogen bonds within a structure and it should allow to monitor the change in the HB network throughout a reaction. Credit to the person who wrote it. Especially, lines 61 to 69 make heavy use of iterate, but I cant quite follow it. Understanding 'iterate' (and naturally iterate_state, alter and alter_state), I believe, would help me alot in writing better scripts. Anyway, thanks again for the support. Martin On 25.10.10 12:49, Tsjerk Wassenaar wrote: > Never get used to that only-reply-to-sender policy... > > > ---------- Forwarded message ---------- > From: Tsjerk Wassenaar<tsje...@gmail.com> > Date: Mon, Oct 25, 2010 at 12:30 PM > Subject: Re: [PyMOL] What is the difference between Atom ID and Index > To: Martin Hediger<ma....@bluewin.ch> > > > Hi Martin, > > ID is indeed the atom id from the coordinate (PDB) file. Index, AFAIK, > is the atom index in the model, starting from 1. > > Probably you should get yourself acquainted with the command line and > with python, as it will help you to solve these and other problems. > For example, you can access properties from the atoms easily through > constructions like these: > > x = [ at.id for at in cmd.get_model(selection).atom ] > y = [ at.index for at in cmd.get_model(selection).atom ] > > That will first build a selection/model object, with a list of atoms > (.atom), over which you can iterate to extract some properties. To > check whether the index is indeed a straightforward list of increasing > numbers, you can then look at the output of > > print y == range(1,len(y)+1) > > Hope it helps :) > > Tsjerk > > On Mon, Oct 25, 2010 at 10:55 AM, Martin Hediger<ma....@bluewin.ch> wrote: >> Dear All >> I'm trying to figure out for myself, what the two labels 'Label> Atom >> Identifiers> ID' and 'Label> Atom Identifiers> index' mean, or what >> the respective difference between the two is. For sure, the numerical >> value is very different when I show the labels in a structure. ID seems >> to be the index of the atom in the list of atom-descriptor lines in the >> PDB input file. But I cant figure out what 'index' is referring to. >> >> Any help on this would be very welcome. >> >> Martin >> >> ------------------------------------------------------------------------------ >> Nokia and AT&T present the 2010 Calling All Innovators-North America contest >> Create new apps& games for the Nokia N8 for consumers in U.S. and Canada >> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing >> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store >> http://p.sf.net/sfu/nokia-dev2dev >> _______________________________________________ >> 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 >> > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Molecular Dynamics Group > * Groningen Institute for Biomolecular Research and Biotechnology > * Zernike Institute for Advanced Materials > University of Groningen > The Netherlands > > > ------------------------------------------------------------------------------ Nokia and AT&T present the 2010 Calling All Innovators-North America contest Create new apps & games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev _______________________________________________ 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
