[chimerax-users] smoother spheres, custom contact distance

[Elaine Meng]

> On Jan 18, 2022, at 3:08 AM, Enrico Martinez via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> 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?

I don't understand what you mean by displayed layer.  Graphics window?  List of results in the Log? The contacts command works on atoms, whereas residues have multiple atoms -- so if there are multiple atoms in the residue that contact the ligand, you will see multiple lines.  If you mean the same two atoms are listed twice in the Log for H-bonds, it means it could be donor->acceptor or acceptor<-donor.  You can only control the atomic parameters, there is no option to only draw one line per residue.

>> 
>> 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?

(you already figured this out, as you said above)

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

See "set subdivision"
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/set.html#subdivision>
... or "graphics quality" and its "atomTriangles" option:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#quality>

>> 
>> 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
>> 

You should check the help for the command you are already using.  E.g. just use command "help contacts" to see the help page for "contacts".  You can specify the VDW surface contact cutoff with the "overlapCutoff" option, or if you don't care about the different atomic sizes and only want to use center-center distances, see the "distanceOnly" option.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco