Hi Daniel,
You say you used "split_states", so all your conformations have the same
topology (are the same molecule). In that case, I suggest to use cmd.rms
instead of cmd.align, which will be more efficient. You also don't need to
split the structures, but call the function with the correct "mobile_state" and
"target_state" arguments. The cmd.rms() function returns the RMSD. Note that it
by default calculates the all-atom RMSD, vs. cmd.align which does outlier
rejection.
Example:
python
from pymol import cmd
f=open('rmsd.txt','w')
cmd.fetch('1nmr')
for state in range(2, cmd.count_states() + 1):
r = cmd.rms('1nmr and name CA',
'1nmr and name CA', 1, state)
f.write('State: %3d RMS: %5.2f\n' % (state, r))
f.close()
python end
Hope that helps.
Cheers,
Thomas
On 03 Dec 2015, at 17:13, Daniel Munoz Escudero wrote:
> Hi!
>
> I have a group of structures (168 in total) and I want to align all of them
> to the first one in order to know the RMSD calculation. For that purpose I
> use the following:
>
> f=open('rmsd.txt','w')
> rms2=cmd.align('structure_0002 and name ca','structure_0001 and name ca')
> .
> . (NOTE: I got all of these structures by the command split_states somename)
> .
> rms9=cmd.align('structure_0009 and name ca','structure_0001 and name ca')
>
> How do I get the output with the number of each RMSD into the text file
> rmsd.txt? What other way can I use to do so?
>
> Thanks in advance,
> D.
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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