Hi all,

Can anyone help me with a problem that I am having trying to run a python script?
I am trying to run the bbPlane script from the PyMOLWiki <http://www.pymolwiki.org/index.php/BbPlane>
I have copied the script from the web page, to a plain text document, saved it as "bbPlane.py" but when I run it I get:

PyMOL>run bbPlane.py
Traceback (most recent call last):
  File "/Volumes/Port 3/software/MacPyMOL.app/pymol/modules/pymol/parser.py", line 332, in parse
  File "/Volumes/Port 3/software/MacPyMOL.app/pymol/modules/pymol/parsing.py", line 455, in run_file
  File "bbPlane.py", line 14
 SyntaxError: invalid syntax 

script is here:
# -- bbPlane.py - draws a CGO plane across the backbone atoms of
#                 neighboring amino acids
# Author: Jason Vertrees, 06/2010
#   Modified by Thomas Holder, 06/2010
#   Modified by Blaine Bell, 08/2011
# Copyright (C) Schrodinger
# Open Source License: MIT
from pymol.cgo import *    # get constants
from pymol import cmd, stored
from chempy import cpv
def bbPlane(objSel='(all)', color='white', transp=0.0):
    Draws a plane across the backbone for a selection
    objSel = string: protein object or selection {default: (all)}
    color = string: color name or number {default: white}
    transp = float: transparency component (0.0--1.0) {default: 0.0}
    You need to pass in an object or selection with at least two
    amino acids.  The plane spans CA_i, O_i, N-H_(i+1), and CA_(i+1)
    # format input
    transp = float(transp)
    stored.AAs = []
    coords = dict()
    # need hydrogens on peptide nitrogen
    cmd.h_add('(%s) and n. N' % objSel)
    # get the list of residue ids
    for obj in cmd.get_object_list(objSel):
        sel = obj + " and (" + objSel + ")"
        for a in cmd.get_model(sel + " and n. CA").atom:
            key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
            coords[key] = [a.coord,None,None]
        for a in cmd.get_model(sel + " and n. O").atom:
            key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
            if key in coords:
                coords[key][1] = a.coord
        for a in cmd.get_model("(hydro or n. CD) and nbr. (" + sel + " and n. N)").atom:
            key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
            if key in coords:
                coords[key][2] = a.coord
    # need at least two amino acids
    if len(stored.AAs) <= 1:
        print "ERROR: Please provide at least two amino acids, the alpha-carbon on the 2nd is needed."
    # prepare the cgo
    obj = [
    for res in range(0, len(stored.AAs)-1):
        curIdx, nextIdx = str(stored.AAs[res]), str(stored.AAs[res+1])
        # populate the position array
        pos = [coords[curIdx][0], coords[curIdx][1], coords[nextIdx][2], coords[nextIdx][0]]
        # if the data are incomplete for any residues, ignore
        if None in pos:
            print 'peptide bond %s -> %s incomplete' % (curIdx, nextIdx)
        if cpv.distance(pos[0], pos[3]) > 4.0:
            print '%s and %s not adjacent' % (curIdx, nextIdx)
        # need to order vertices to generate correct triangles for plane
        #      modified/added by B.Bell 8/18/2011
        sumpos = cpv.add(pos[0], cpv.add(pos[1], cpv.add(pos[2], pos[3])))
        centerpos = [ sumpos[0]/4., sumpos[1]/4., sumpos[2]/4. ]
        angles = [ [ 0., 0 ] ]
        s00 = cpv.sub(pos[0], centerpos)
        for i in range(1,4):
            s = cpv.sub(pos[i], centerpos)
            ang = cpv.get_angle(s00, s)
            angles.append( [ ang, i] )
        def sortfirst(a, b):
            return cmp(a[0], b[0])
        verts = map(lambda x: x[1], angles)
        vorder = [ verts[0], verts[1], verts[2],
                   verts[1], verts[3], verts[2] ]
        # fill in the vertex data for the triangles; 
        for i in vorder:
    # finish the CGO
    # update the UI
    newName =  cmd.get_unused_name("backbonePlane")
    cmd.load_cgo(obj, newName)
    cmd.set("cgo_transparency", transp, newName)
cmd.extend("bbPlane", bbPlane)


H. Adam Steinberg
Artist, Scientist, Developmental Editor

7904 Bowman Rd
Lodi, WI 53555