Hi folks,
when visualising data out of a GOLD docking run, where the software has added
lone pairs to active site residues and ligands is it possible to remove them
post hoc in Pymol? The "atoms" look like:
62 **** 45.6415 30.9229 12.1185 LP 1 <1>
0.0000
in the output .mol2 files so the **** "atom" names are clearly not going to be
helpful in a command line situation. For a single ligand pose it's not too bad
doing it by hand but for multiple poses of multiple ligands it gets pretty old
pretty fast. Usually I just tell people to rerun the docking with the GOLD
software told to turn the LPs off but am after a post hoc solution if possible
as people can't always get on to our licenses fast enough to repeat jobs.
GOLD also puts the extra protein LPs into the output ligand file, not into a
modded protein file. those lines in the output ligand files look like:
52.0949 25.2031 14.8408 LP 0 0 0 0 0 0 0 0 0 0 0 0 # atno
4332 bound_to 4006
Any ideas? Thanks,
Martin
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