From: Yamei Yu <ymy...@gm...> - 2011-08-11 23:03:22
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Hi all, I remember in pymol you can move an atom to a specific site and use a command to get the coordinate of this atom. But I for the name of the command. Does any body know? Thank you! Yamei |
From: Jason V. <jas...@sc...> - 2011-08-12 02:35:57
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Hi Yamei, If you need to create an (pseudo)atom at a specific location you can write, pseudoatom objName, pos=[x,y,z] to specify the position. For example, pseudoatom testAtom, pos=[15.0, -22.0, 13.5] Alternatively, if you already have the object, but need to move it you can do, translate [x,y,z], objectName For example, translate [-10, 3, 5.6], myProtein To get atomic coordinates you can use iterate_state: iterate_state 1, myObj, print x,y,z or you can get the indexed chempy model and print its coordinates: print cmd.get_model("myObj").atom[0].coord For more information, please check the following pages on the PyMOLWiki: http://www.pymolwiki.org/index.php/Pseudoatom http://www.pymolwiki.org/index.php/Translate http://www.pymolwiki.org/index.php/Iterate_State Cheers, -- Jason On Thu, Aug 11, 2011 at 7:03 PM, Yamei Yu <ymy...@gm...> wrote: > Hi all, > > I remember in pymol you can move an atom to a specific site and use a > command to get the coordinate of this atom. But I for the name of the > command. Does any body know? > > Thank you! > > Yamei > > ------------------------------------------------------------------------------ > Get a FREE DOWNLOAD! and learn more about uberSVN rich system, > user administration capabilities and model configuration. Take > the hassle out of deploying and managing Subversion and the > tools developers use with it. > http://p.sf.net/sfu/wandisco-dev2dev > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |