Re: [PyMOL] syntax for lone pair removal

[Thomas H. <sp...@us...>]

Hi Martin,

> 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

the atom_type field after the x/y/z coordinates says "LP", which will be 
loaded as the element symbol into PyMOL. So this should work:

remove elem LP

> 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

this is a SDF file, right? So you can remove by name:

remove name LP

Cheeres,
   Thomas

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen