rms and fit gave you different values? They have never given me different
values.
Example:
from pymol import cmd
cmd.fetch('1nmr')
cmd.split_states('1nmr')
for i in xrange(1,21):
for j in xrange(1,21):
prot_i = '1nmr_%04d' %i
prot_j = '1nmr_%04d' %j
rms_val = cmd.rms(prot_i, prot_j)
fit_val = cmd.fit(prot_i, prot_j)
print rms_val-fit_val
prints 400 lines of 0.0
-David
On Wed, Apr 14, 2010 at 11:29 AM, Renuka Robert <renukarob...@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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------------------------------------------------------------------------------
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proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
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