[chimerax-users] Surface representation of protein-ligand interactions

[Enrico Martinez]

Dear ChimeraX users!
I am working on the surface representation of the protein-ligand
contacts. Here is my script:

# load pdb of the complex and keep inly the 1st model
open pdb.pdb
close #1.2-end

#calculate electrostatic surface
coulombic protein key true

#change view of the ligand
size ligand atomRadius +.8
color #1.1 & ligand & C gold
style ligand sphere

#protein-ligand contacts
hbonds #1.1 & ligand reveal true log true
contacts #1.1 & ligand makePseudobonds false reveal true log true
label @@display height 0.8 color orange
~label ligand
hide #1 & protein bonds
hide #1 & protein pseudobonds

Here are my questions:
1) is it possible to set transparency on the part of the displayed
surface that overlaps (hide) with the part of the displayed ligand?

i've tried: transparency 20 surface,
but it change the transparency for whole surface

2) how I may improve further sphere representation of the ligand? it
looks very nice but probably there are further modifications ?

3) is it possible to customize the following commands to display
amino-acids that within specified distance within the ligand (I would
like to display only very closer amino-acids):
contacts #1.1 & ligand makePseudobonds false reveal true log true
label @@display height 0.8 color orange

Many thanks in advance!
Cheers
Enrico