Re: [PyMOL] Getting information fron selected objects
Hi Phil, one option to get access to the coordinates is using the chempy model of a given selection ( named (sele) if you clicked it). m = cmd.get_model((sele)) the chempy model contains a list of atom objects which contain most properties you might need. for atom in m.atom: print atom.id, atom.name, atom.resn, atom.resi, atom.coord To extract the coordinates of all atoms you can simple do: coords = map(lambda a: a.coord, m.atom) or if you need the coordinates as numpy arrays use: from numpy import * coords = map(lambda a: array(a.coord), m.atom) gives you a list of numpy arrays or: coords = matrix(map(lambda a: a.coord, m.atom)) will produce a numpy matrix with your coords. Then you might do whatever you want with the coordinates and update the coordinates of the chempy model. As far as I now, you can not transfer them back easily to PyMOL but you can do a little trick. Load the modified model as new pymol object: cmd.load_model(m,modified) and then update the original selection with the coords from the modified object. cmd.update((sele),modified) Then you can delete the modified object. cmd.delete(modified) Cheers, Daniel On Tuesday 19 January 2010 08:00:51 pm Phil Payne Local wrote: I am writing a Pymol plugin, in which I need to extract, manipulate, and replace the coordinates of selected atoms. Are there examples out there I could use as a prototype? For starters, what command(s) do I use to get the name strings of residues that I've selected with mouse clicks. I would like to assign these to a variable. Then the same question applies to coordinates. How do I assign the values of atomic coordinates to a list variable in my plug_in script? --- --- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-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 -- Dr. Daniel Seeliger Computational Biomolecular Dynamics Group Max-Planck-Institute for Biophysical Chemistry Tel. +49 (0) 551-201-2310 http://wwwuser.gwdg.de/~dseelig -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-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
[PyMOL] Getting information fron selected objects
I am writing a Pymol plugin, in which I need to extract, manipulate, and replace the coordinates of selected atoms. Are there examples out there I could use as a prototype? For starters, what command(s) do I use to get the name strings of residues that I've selected with mouse clicks. I would like to assign these to a variable. Then the same question applies to coordinates. How do I assign the values of atomic coordinates to a list variable in my plug_in script? -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-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
Re: [PyMOL] Getting information fron selected objects
Phil, The answers to your questions lie in the iterate, iterate_state, alter, and alter_state commands. The PyMOLWiki has extensive documentation on these commands (http://pymolwiki.org/index.php/Iterate). Once you select something with the mouse you can get information using iterate/alter. # make mouse selection; the (sele) selection is created # create a copy selection called myCopy select myCopy, (sele) # count atoms in myCopy print cmd.count_atoms(myCopy) # see what atom IDs are in the selection iterate myCopy, print ID Hope this helps, -- Jason On Tue, Jan 19, 2010 at 2:00 PM, Phil Payne Local ppa...@maxwell.compbio.ucsf.edu wrote: I am writing a Pymol plugin, in which I need to extract, manipulate, and replace the coordinates of selected atoms. Are there examples out there I could use as a prototype? For starters, what command(s) do I use to get the name strings of residues that I've selected with mouse clicks. I would like to assign these to a variable. Then the same question applies to coordinates. How do I assign the values of atomic coordinates to a list variable in my plug_in script? -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-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 -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-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
