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@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