Hi Paul,
I have a set of active atoms (GOLD output) that surround a cavity. Now I
want to dipslay the surface only for the cavity wall, not on the
outside.
try this: show surface for the whole protein and then hide surface for
"not the active residues" - something like this:
####
from pymol import cmd
from pymol import stored
# load your protein and the active atoms as GOLD output
cmd.load("protein.pdb", "prot")
cmd.load("active_atoms.pdb", "act_res")
# create a list of the activ residue-id's stored.act_res=[]
cmd.iterate("act_res", "stored.act_res.append(resi)")
# create selection of the actives
cmd.select("act_res","resi %s" %stored.act_res[0])
for i in stored.act_res:
cmd.select("act_res","act_res or resi %s" %i)
# create selection of the "non-actives"
cmd.select("not_act_res", "prot and not act_res")
# show surface
cmd.show("surface", "prot")
cmd.hide("surface", "not_act_res" )
cmd.delete("not_act_res")
####
Cheers,
Betty
