Dear Krisztina,

alternatively you could use Xwalk for visualizing distance constraints on PDB structures. Please have a look at the webserver (www.xwalk.org) or download the software if you find it useful (http://www.xwalk.org/cgi-bin/download.cgi).

With Xwalk you can calculate surface distances and Euclidean distances between atoms in PDB structures. For visualisation purposes it produces .pml PyMol scripts, which might be exactly what you are looking for. For targeted distance calculation all you need to do is provide Xwalk your PDB structure and a text file with a list of the atom pairs. The text file has to have the following format:

index\tproteinName\tAtomIdentifier1\tAtomIdentifier2

e.g:
1 test.pdb LYS-1-A-CA LYS-2-A-CA
2 test.pdb LYS-4-A-CA LYS-10-A-CA
...

Once you have your text file ready, simply run Xwalk as follows:

> java Xwalk -infile test.pdb -dist noe.txt -euc -pymol -out test_noe.pml

You can also try "java Xwalk -help" to get further information about additional commandline parameters. After Xwalk has finished its calculation, open the test_noe.pml file with PyMol.

Let me know if you need any further assistance.
Abdullah




On 29 Oct 2012, at 16:02, Krisztina Feher <feher_krisztina@yahoo.com> wrote:

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_krisztina@yahoo.com> wrote:

From: Krisztina Feher <feher_krisztina@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-----

------------------------------------------------------------------------------
WINDOWS 8 is here.
Millions of people.  Your app in 30 days.
Visit The Windows 8 Center at Sourceforge for all your go to resources.
http://windows8center.sourceforge.net/
join-generation-app-and-make-money-coding-fast/

-----Inline Attachment Follows-----

<plot_noe.py>------------------------------------------------------------------------------
The Windows 8 Center - In partnership with Sourceforge
Your idea - your app - 30 days.
Get started!
http://windows8center.sourceforge.net/
what-html-developers-need-to-know-about-coding-windows-8-metro-style-apps/_______________________________________________
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

--<------<---@
Abdullah Kahraman, PhD
Aebersold - Malmstroem Group
Institute of Molecular Systems Biology
ETH Zurich
HPT C75
Wolfgang-Pauli-Str. 16
8093 Zurich
Switzerland

work: +41-(0)44-633 66 71
mobile: +41-(0)76-317 0305