Dear All,
When I run the centroid.py, I have the following error message: "NameError: global name 'move' is not defined". My centroid.py script downloaded (have I misdone or miseddited something?) is as following. Will you please tell me how to solve the error message issue? Smith --- See more here: http://www.pymolwiki.org/index.php/centroid DESCRIPTION get the centroid (geometric center) of a selection or move selection to the origin. ARGUMENTS selection = string: a valid PyMOL selection {default: all} center = 0 or 1: if center=1 center the selection {default: 0} returns: centroid: [ x, y, z ] SEE ALSO get_extent, get_position, http://pymolwiki.org/index.php/Center_Of_Mass # @AUTHOR: Jason Vertrees # Copyright (c) 2008, Jason Vertrees # All rights reserved. # # Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following # conditions are met: # # * Redistributions of source code must retain the above copyright notice, this list of conditions and the following # * disclaimer. # * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following # * disclaimer in the documentation and/or other materials provided with the distribution. # * Neither the name of the <ORGANIZATION> nor the names of its contributors may be used to endorse or promote products derived # * from this software without specific prior written permission. # # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT # NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL # THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES # (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS # INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE # OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. # # DATE : 2008-09-26 # REV : 1 ''' from pymol import cmd from pymol import stored from chempy import cpv def centroid(selection='all', center=0, quiet=1): model = cmd.get_model(selection) nAtom = len(model.atom) centroid = cpv.get_null() for a in model.atom: centroid = cpv.add(centroid, a.coord) centroid = cpv.scale(centroid, 1. / nAtom) if not int(quiet): print ' centroid: [%8.3f,%8.3f,%8.3f]' % tuple(centroid) if int(move): cmd.alter_state(1, selection, "(x,y,z)=sub((x,y,z), centroid)", space={'centroid': centroid, 'sub': cpv.sub}) return centroid cmd.extend("centroid", centroid)
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