Mike,
As for NMR ensembles, so long as all of the structures loaded as multiple
states in a single object (the default behavior for NMR ensembles in
multi-model PDB format):
print cmd.intra_fit(selection, state)
will fit all of the other states to the indicated states and return the RMS
values as a list. For example:
fetch 1i8e, async=0
print cmd.intra_fit("1i8e////CA", 1)
[-1.0, 1.1934459209442139, 1.2950557470321655, 0.71329855918884277,
0.76704370975494385, 0.78973227739334106, 0.99323123693466187,
1.0165935754776001, 0.6535714864730835, 0.95591926574707031,
1.1299723386764526, 0.28637325763702393, 0.69836461544036865,
0.40816938877105713, 1.1637680530548096]
Note that a RMS value of -1.0 is returned for the target state.
As for writing results to a file, Python provides a rich set of capabilities
for this sort of thing. For example:
fetch 1i8e, async=0
list = cmd.intra_fit("1i8e////CA",1)
output=open("output.txt",'wa')
for rms in list: output.write(str(rms)+"\n")
output.close()
Cheers,
Warren
--
DeLano Scientific LLC
Subscriber Support Services
mailto:[email protected]
> -----Original Message-----
> From: [email protected]
> [mailto:[email protected]] On Behalf
> Of Michael Summers
> Sent: Wednesday, February 13, 2008 8:59 AM
> To: [email protected]
> Subject: [PyMOL] help with batch mode
>
> Colleagues,
>
> Does anyone have a good method for generating alignment
> statistics in batch mode using pymol?
>
> I think I'd like to do something like:
>
> pymol -c sup.py > data.txt
>
> where sup.py is something like:
>
> load ./final/final.001.pdb
> load ./final/final.002.pdb
> fit (final.002///13-30/c,ca,n), (final.001///13-30/c,ca,n)
>
>
> The problem is that I only seem to be able to launch python
> scripts automatically at startup (cmd.xxxx commands) in this
> manner, and I don't know how to capture the RMS output.
>
> Interestingly, if I add the above "load" and "fit" statements
> to my .pymolrc file, and I run "pymol -c > output.txt", I do
> get the output I want in the output.txt file. I'm sure there
> must be a way of doing this without having to edit my .pymolrc file,
>
>
> Better yet, has someone worked out a convenient way to
> generate RMS statistics for NMR ensembles using pymol?
>
> Many thanks,
>
> Mike
>
>
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