Hello,
Just remove the following from the script, since it is, apparently,
obsolete:
if int(move):
cmd.alter_state(1, selection, "(x,y,z)=sub((x,y,z), centroid)",
space={'centroid': centroid, 'sub': cpv.sub})
Or just download again the script, they already removed these lines
themselves:
https://raw.githubusercontent.com/Pymol-Scripts/Pymol-script-repo/master/centroid.py
---------
2015-11-20 4:00 GMT+02:00 Smith Liu <[email protected]>:
> 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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