Dear Pymol users!
I have a folder with many pdb files. I would like to use pymol in
no-gui mode in order to i)load all pdb within the pymol; ii)
superimpose each pdb agains the first (top) pdb; iii) save sperimposed
pdbs into the new folder under the SAME names of pdbs.
Here is model of my script, which should be modified according to the
indicated commentaries (mostly on the step of saving results).
${pymol} -c -d "
from pymol import cmd
# we open at once all pdbs which have "B-factors" suffix in its name!
cmd.load('${output}/!temp/B-factors*')
# it do almost what I want in terms of the superimposition, however
not all snapshots are aligned properly
cmd.extra_fit('name CA', '*', 'super')
# here the most tricky part that should be modified since I need to
save snapshots using some command keeping its original names!
cmd.save('output' + '.pdb')
"
so the task is that I would like to use it in one command rather then
to put inside the loop (e.g. opening 2 snapshots for each time to make
mobile, reference superimposition, which is more easy way).
Thank you in advance!
James
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