[chimerax-users] Making New Bonds between Protein & Ligand

[Elaine Meng]

Hi Arun,
As the message says, you can only add bonds between atoms that are in the same model, not separate models.   This is if you want to add a real (covalent) bond.  If this is just for display purposes you can instead draw a pseudobond between the two separate models.
<http://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html>

To add a covalent bond, you need to first combine the ligand and protein into a single model.

ChimeraX does not have a "combine models" function but you could do that in Chimera:  i.e. open the protein and ligand structures, look in Model Panel (open from Chimera menu: Favorites) to check the model numbers, and use the "copy/combine" function in the Model Panel after choosing those models, or the Chimera command "combine" to combine them into a single model.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html>

If you're using Chimera already, you can just add the bond (to the new combined model, again the atoms have to be in the same model) in that program with command "bond," 
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/bond.html>
...or you can save a PDB file of the new single model, then open that PDB in ChimeraX, then use the marker link trick.

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

> On Apr 8, 2020, at 10:46 AM, Gupta, Arun <Arun.Gupta at warwick.ac.uk> wrote:
> 
> Hi 
> I followed similar " marker link "  trick proposed by Tom for making new  bonds between a selection of  Serine residue of protein molecule with hydroxy group functionality of ligand molecule typing the below mentioned  command  in ChimeraX command line . 
> 
> marker link #1:54 at OG #2:PNS at HOP1@SG radius 0.2
> 
> However, I am repeatedly getting following error.  " TypeError: Cannot bond atoms in different molecules "
> 
> Can you plz suggest the correct command or alternative way for making new bond between Protein & ligand molecules.  
> 
> Thanks
> Arun