Hi Thomas,
thanks a lot for your reply! Now I was running the
script from command line and executed it: it did not display anything on
the structure. I inserted a couple of print statements into the script
(attached), but it seems that the "noe_regex" is not being found in the
variable "line" by the .search method (see the output below: match is
None). The pdb file does have residue 433 and all the listed atom names.
The noe_regex looks sort of complicated, I have no idea how to fix it.
If anyone had an idea how to fix it, I would very much appreciate it.
Thanks,
Krisztina
ps. If this script works for on your
system, please write me too!
--- On Sun, 10/28/12, Krisztina Feher <feher_kriszt...@yahoo.com> wrote:
From: Krisztina Feher <feher_kriszt...@yahoo.com>
Subject: [PyMOL] visualise NOEs
To: pymol-users@lists.sourceforge.net
Date: Sunday, October 28, 2012, 10:14 PM
Hi,
I am looking for a script that could show CNS type distance restraints on a pdb
structure. In fact I have found a script on Justin Lorieau's homepage
(http://www.lorieau.com/software/biophysics-software/40-plot-xplor-noes-in-pymol.html)
that seems to intend to do exactly what I want, but it does not seem to work
(I have Pymol 1.2 version installed with package manager of Ubuntu). I
installed it as Plugin, but it
gives the message:
Exception in plugin 'plot_noe' -- Traceback follows...
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/pmg_tk/PMGApp.py", line 321, in
initializePlugins
mod.__init__(self)
TypeError: module.__init__() argument 1 must be string, not instance
Error: unable to initialize plugin 'plot_noe'.
Upon execution with a distance .tbl file nothing happens
on the structure. I attached the script, I would appreciate any ideas how to
make it work.
Thanks a lot!
Krisztina
-----Inline Attachment Follows-----
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# plot_noe
#
# Written by Justin L Lorieau
# Version 20110923
from pymol import cmd
def plot_noe(filename, line_color='black', line_width='1.0', replace_pound='2'):
"""A function for plotting XPLOR NOE restraints on a structure using an impressive,
yet highly limited, regex for parsing.
:filename:
The filename of the NOE retraint file in XPLOR NIH format.
:line_color:
The color for the NOE lines. See the standard colors in PyMOL.
Default: 'black'
:line_width:
The thickness of the NOE lines.
Default: '1.0'
:replace_pound:
Replace the '#' character with the following character.
Default: '2'
NOE Restraint Format
--------------------
assign (residue 5 and name HB#) (residue 21 and name HA) 3.0 0.7 0.7 # long
# assign (residue 3 and name HA) (residue 3 and name HB#) 2.2 0.3 0.3
Usage Notes
-----------
Commented 'assign' lines are skipped
This function cannot handle nested parentheses well. Please assign these to
one group or another. Also this function does not handle ranges with a ':'.
All atom groups denoted with a '#' are replaced with the replace_pound
character.
Usage Example
-------------
PyMOL> plot_noe noe_short.tbl
"""
from pymol import cmd
import re
noe_regex = re.compile(r"""\s*[^#]\s*assign\s*\((?P<group1>[^\)]+)\)(\s*assign\s*)?\((?P<group2>[^\)]+)\)\s*(?P<dist>\d+(\.\d+)?)""")
resid_regex = re.compile(r"resid(ue)?\s*(?P<resid>\d+)")
name_regex = re.compile(r"name\s*(?P<name>[\w\#]+)")
count = 0
with open(filename) as f:
for line in f.readlines():
print line
print noe_regex.search(line)
match = noe_regex.search(line)
print match
if match is None:
continue
# Parse the assignments in each group
# ex: match['group1'] = 'residue 21 and name HB#'
group1 = match.groupdict()['group1']
group2 = match.groupdict()['group2']
dist = match.groupdict()['dist']
# Parse the residue number and atom names
name1 = name_regex.search(group1).groupdict()['name'].replace('#',replace_pound)
name2 = name_regex.search(group2).groupdict()['name'].replace('#',replace_pound)
resid1 = resid_regex.search(group1).groupdict()['resid']
resid2 = resid_regex.search(group2).groupdict()['resid']
#resid1, resid2 = map(float, (resid1, resid2))
count += 1
print group2
# Create the PyMOL restraint
label = "NOE_" + str(count)
cmd.do("".join(("distance ", label, ", ",
resid1, "/", name1, ", ",
resid2, "/", name2)))
# Format the line
cmd.do("set dash_color, " + line_color + ", " + label)
cmd.do("set dash_gap, 0, " + label)
cmd.do("set dash_width, " + line_width + ", " + label)
cmd.do("hide labels")
cmd.extend("plot_noe",plot_noe)
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