Hi Smith, There was an error in script, incidentally, I introduce the error, but now is fixed. Please download again the centroid.py script.
Cheers, Osvaldo. On Fri, Nov 20, 2015 at 3:00 AM, Smith Liu <smith_liu...@163.com> wrote: > 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) > > > > > > > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > 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 >
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