Re: [PyMOL] bbPlane script "SyntaxError: invalid syntax"

Hi Adam,

Here's an alternative script... The command is pplanes (peptide-planes):

run triangles.py
pplanes selection[, color[, alpha[, state[, name]]]]

Hope it helps,

Tsjerk


On Thu, Aug 25, 2011 at 5:34 PM, H. Adam Steinberg <ad...@st...> wrote:
> 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
> <" rel="nofollow">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):
>     """
> DESCRIPTION
>
>     Draws a plane across the backbone for a selection
>
> ARGUMENTS
>
>     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}
>
> NOTES
>
>     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)
>             stored.AAs.append(key)
>             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."
>         return
>
>     # prepare the cgo
>     obj = [
>         BEGIN, TRIANGLES,
>         COLOR,
>         ]
>     obj.extend(cmd.get_color_tuple(color))
>
>     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)
>             continue
>
>         if cpv.distance(pos[0], pos[3]) > 4.0:
>             print '%s and %s not adjacent' % (curIdx, nextIdx)
>             continue
>
>         # 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])
>         angles.sort(sortfirst)
>         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:
>             obj.append(VERTEX)
>             obj.extend(pos[i])
>
>     # finish the CGO
>     obj.append(END)
>
>     # update the UI
>     newName =  cmd.get_unused_name("backbonePlane")
>     cmd.load_cgo(obj, newName)
>     cmd.set("cgo_transparency", transp, newName)
>
>
> cmd.extend("bbPlane", bbPlane)
>
> artforscience
> H. Adam Steinberg
> Artist, Scientist, Developmental Editor
> www.artforscience.com
> 7904 Bowman Rd
> Lodi, WI 53555
> 608/729-5944
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands