Hi Renuka,

With a little bit of Python programming and better understanding of structure alignment in PyMOL you should be able to complete your task.  First, check out the structure alignment category on the PyMOLWiki (http://www.pymolwiki.org/index.php/Category:Structure_Alignment).  Read the difference between fitting (eg. 'fit') and aligning (eg. 'align').  PyMOL also comes with built-in help, so try "help align" to get help and details on the 'align' command.  For pairwise aligning check out the "alignto" command on the "cealign" webpage in the PyMOLWiki--this will show you how to iterate over loaded proteins and align them to one target.

Here's some code to start with:

#start Python in PyMOL
python

# get the list of objects
p = cmd.get_names("objects")

# create the dictionary of results
results = {}
for curO in p:
  if curO not in results: results[curO] = {}
  for curI in p:
    results[curO][curI] = cmd.align(curO, curI, cycles=0)

import pprint
pprint.pprint(results)

# stop python in PyMOL
python end

Cheers,

-- Jason



On Wed, Apr 14, 2010 at 11:29 AM, Renuka Robert <renukarobert@ymail.com> wrote:
Hi  All Pymol users

I have a set of 40 X-ray crystallographic structures complexed with inhibitors belonging to a specific family of kinases. Binding site residues within 5 angstrom from the inhibitor were selected for each PDB structure and saved separately. Now i have a set of 40 PDB files which has only the binding site residues.


I want to perform RMSD for ALL ATOMS against ALL ATOMS. The first structure should be fixed and compared with the remaining 39 structures. For the next time, second structure is fixed and so on for all the 40 structures. Literally it should look like a 40X40 matrix table.


I used align, fit and rms commands. Each one gives different values. Which is the best? Can you help me?


Thank you in advance

Renuka



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--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jason.Vertrees@schrodinger.com
(o) +1 (603) 374-7120