Dear PyMol users,
I would like to integrate pymol in my scripting workflow in order to
save images/pymol sessions of different protein-ligand complexes.
Notably I have a typical autodock output in multi-model format of 20
ligand poses and 1 snapshot of the protein. I need to execute from the
terminal the sequence of pymol commands integrated in a simple bash
workflow:
for pdb in "${storage}"/"${experiment}"/*.pdb ; do
pdb_name=$(basename "$pdb" .pdb)
pymol $pdb
done
The final aim is to make visualization between protein and each of the
ligand model on the same plane (to see ligand clusters obtained from
autodock)
Here what I do in pymol GUI:
load $pdb
set white background # set white background
dss # show ss of the protein in cartoon
split states complex* # the beginning of pdb name is "complex"
select polymer
color gray # color polymer in gray
select not polymer
show as stics # show ligand as stics
save current session in pse
# optionally: colour each of the ligand cluster by individual colour#
png ${pdb_name} # make a nice png of the protein bound to 20 different
conformations :-)
Is it possible to run all of these commands in terminal or
alternatively providing some sort of batch file recognized by pymol (i
am working in mac with an educational version of pymol) ?
Thank you in advance for any suggestions!
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