[Chimera-users] ligand

[Elaine Meng]

Hello José,
It would not make sense to change the atomic positions (bond lengths) since they are what makes the chemical structure.  

However, maybe you mean you want to make sticks thicker, or if the ligand is shown as ball-and-stick or spheres, make the balls or spheres larger.  
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/representation.html>

There are several different ways to do these things, but one way is to select the whole ligand residue (e.g. with menu: Select... Residue.. [residue name], or by Ctrl-click on the atom followed by pressing the up arrow key) and then click the green magnifying glass to open the Selection Inspector.
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html>

For thicker sticks:  in the Selection Inspector, Inspect: Bond, then change "radius" from 0.2 to something bigger.

Or show ligand (still selected) as ball-and-stick and make the balls bigger, 
command: repr bs sel
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/represent.html>

... and then in Selection Inspector, Inspect: Molecule Model, then change "ball scale" from 0.25 to something bigger.

Or show ligand (still selected) as spheres:
command: repr sphere sel

You probably don't want to make the spheres bigger since the centers will still be in the same place and it will just make the chemical structure harder to understand.  Also, changing the VDW radii will change other calculations like surface area and contacts.  However, if you really want to change the VDW radii you can do it in the Selection Inspector, Inspect: Atoms and change "radii" or using the "vdwdefine" command
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vdwdefine.html>

Of course all of the above can be used on other atoms (receptor sidechains etc.) not necessarily only the ligand.
I hope this helps,
Elaine
----- 
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Mar 18, 2023, at 4:32 AM, José Manuel González Hernández via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hello,
> Is there a way to change features such as width and height of a ligand instead of the ribbons?
> Thanks, José
> 
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