Hey Michael,
with some commands, you can use the (somewhat poorly documented) option
'quiet=0' to get results sent to standard output, like so:
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), quiet=0
Andreas
Michael Summers wrote:
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
-------------------------------------------------------------------------
This SF.net email is sponsored by: Microsoft
Defy all challenges. Microsoft(R) Visual Studio 2008.
http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
_______________________________________________
PyMOL-users mailing list
PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users
