P.S. sorry I ought to further precise my question:
From what I have not I can execute pymol in batch mode together with
the py script and pdb
pymol my.pdb center_of_mass.py -d 'select all;com all' -c >> log.txt
which gives me log.txt contained COM for each model in the following format:
State 1:118.851979 120.668604 84.472229
State 2:126.789728 149.506520 103.196917
State 3:126.379687 149.382354 104.504792
State 4:126.989312 149.372811 103.499396
.....
State 20:125.555854 133.653730 88.441501
Obviously I can pipe this output to another program to convert it into
the list format, but
is it possible rather to modify the python script, automatically
loading all pdbs located from the current directory and save the
output automatically in the list format indicated in my first message?
сб, 7 нояб. 2020 г. в 14:16, Jeff Saxon <jmsstarli...@gmail.com>:
>
> Dear Pymol Users,
> I am using the Centre of mass python script found in PymolWIKI with
> the aim to calculate the centre of mass of the loaded ligand
> structure. Could you tell me if it would be possible to apply this
> script on the multi_model pdb loaded in pymol in the similar way and
> to obtain XYZ coordinates of COM for each conformation? Is it possible
> to do it in some scripting manner using no-gui pymol and save output
> in the list format like {[name the conformation_1],[x,y,z].... name of
> the conformation_N,[x,y,z]}?
> Thank you in advance
> Cheers,
> J.
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