From: Sajeewa P. <saj...@gm...> - 2012-11-21 16:46:27
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Hi all, I want to place copies of CO2 along a tunnel created by PyMol CAVER. Is there any way I can get the xyz coordinates of the pseudo-atoms that comprise the tunnel, when I select the pseudo-atoms I want? Thank you Sajeewa Dewage |
From: Jason V. <jas...@sc...> - 2012-11-21 17:40:29
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Hi Sajeewa, > I want to place copies of CO2 along a tunnel created by PyMol CAVER. Is there any way I can get the xyz coordinates of the pseudo-atoms that comprise the tunnel, when I select the pseudo-atoms I want? Assuming the pseudoatoms are real PyMOL "pseudoatoms" (http://www.pymolwiki.org/index.php/Pseudoatom) then you have two choices: (1) One at a time # print the atomic coords of the pseudoatom 'caver1' print cmd.get_atom_coords("caver1") (2) Many at once # get the model for the object/selection 'caver1' m = cmd.get_model("caver1") # print the list of coordinates for all atoms/pseudoatoms # in the object/selection 'caver1' print map(lambda a: a.coord, m.atom) Cheers, -- Jason -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) Jas...@sc... (o) +1 (603) 374-7120 |