Dear Pymol Users!
I am dealing with the multi-model pdb containing the docking poses
that were merged with the protein atoms. Initially the part containing
the ligand poses also included some flexible side-chains of the
receptor (obtained from VINA) that were subsequently merged ( in each
model) with the static part of the protein using some script.
The complex may be correctly visualised in pymol, however (due to the
reorganizations of the atoms in the protein part) there are some
problems in the visualisations of the interatomic interactions between
the static part of the protein and the ligands.
May we use some pymol in no-gui mode to "fix" the atomic order problem
in the loaded pdb (in each models!) and then save it as a new pdb?
Here is the model of the workflow:
pymol -c -d "
from pymol import cmddb')
cmd.load('complex.pdb')
# execute some command to fix atom order in the multi-model pdb
cmd.save('complex_fixed_pdb.pdb')
"
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