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

[Enrico Martinez]

P.S. First, please ignore my question regarding surface transparency
since I've just found it!
just additional question about contacts
contacts #1.1 & ligand
why sometimes I could see on the displayed layer the same residue two
times? Does it mean two possible interactions with the ligand ? May I
suppress the replicas from the contacts layer?
Cheers,
Enrico

вт, 18 янв. 2022 г. в 10:06, Enrico Martinez <jmsstarlight at gmail.com>:
>
> 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