Tristan’s answer is the only way to go in ChimeraX right now. Adding bonds via a tool or command is among the missing features we just haven’t gotten to yet. Alternatively, you could open your structure in Chiimera, make the the bond, and write out a PDB you could then open in ChimeraX.

If you are going to be adding more than one bond, you can make Tristan’s method a little easier to access by turning the Python code into a “preset”. You would save his code into a file, and then follow the instructions in Presets→Add A Preset… to turn it into a preset (probably named something like “New Bond”). To use it you would then select two atoms and choose the New Bond preset.

On Apr 7, 2020, at 8:30 AM, Tristan Croll <tic20@cam.ac.uk> wrote:

Currently, I think the shell is your friend here. First, select the two sulfurs. Then, in the shell:

from chimerax.atomic import selected_atoms
sel=selected_atoms(session)
m = sel.unique_structures[0]
m.new_bond(*sel)

- Tristan

On 7 Apr 2020, at 12:24, Mutum YAikhombA <mutum.yaikhomba@mrc-mbu.cam.ac.uk> wrote:

Hi

I was trying to make new disulphide bonds between a pair of cysteine residues (say residue numbers 142 and 157) using ChimeraX. The standard Chimera command - 'bond' doesn’t work in ChimeraX.
I have gone through the structure editing tool and couldn’t find an equivalent tool. I found some command-line tools in this page (new-bond), but this seems to be not so straightforward to use - https://www.rbvi.ucsf.edu/chimerax/docs/devel/bundles/atomic/src/atomic.html#chimerax.atomic.structure.AtomicStructure.

Could you please help?
Thanks
Yaikhomba
_______________________________________________
ChimeraX-users mailing list
ChimeraX-users@cgl.ucsf.edu
Manage subscription:
http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________
ChimeraX-users mailing list
ChimeraX-users@cgl.ucsf.edu
Manage subscription:
http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users