Hi Rayees, For the best chance at getting a good answer, we recommend sending ChimeraX questions to the chimerax-users list (CC'd here) unless you are including private data. If the two models are already positioned appropriately to form the bond, you could first combine them into a single model and then add a bond (e.g. "bond" command or Build Structure tool, Adjust Bonds section). <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/bond.html> <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#bonds> However, if you didn't necessarily put the models in the right place to form the bond, you can use "build join" which will include all of the following: moving one model to the appropriate position to form the bond, combining the models into one, and forming the bond. You cannot use "build join" if the models are already combined or if you don't want the models to move relative to each other. There is also a graphical interface to "build join," which is the Build Structure tool, Join Models section. <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/build.html#join> <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#join> You can open the Build Structure from the menu under Tools... Structure Editing. <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html> I don't know much about refinement, but sounds like you should take a look at the ISOLDE plugin for ChimeraX. <https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxisolde> <https://isolde.cimr.cam.ac.uk/> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On May 4, 2023, at 11:24 AM, Rayees Mattoo <rmattoo@stanford.edu> wrote:

Hi Elaine, I am trying to merge two models (say #1 and #2) and join the two models with a covalent bond at amino acid residue number say 240 (#1)and 241 (#2). I first combined the two models (#1 and #2) using combine command. However, when I use build join command it does not seem to work. Is there a better way to covalently join two models in chimeraX?

Also, is there a way to refine models in chimeraX like Real Space refine in Coot?

Thanks

Rayees