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
