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@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@OG #2:PNS@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