[chimerax-users] Making new bonds

[Eric Pettersen]

Hi Yaikhomba,
	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.

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Apr 7, 2020, at 8:30 AM, Tristan Croll <tic20 at 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 at mrc-mbu.cam.ac.uk <mailto:mutum.yaikhomba at 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 <https://www.rbvi.ucsf.edu/chimerax/docs/devel/bundles/atomic/src/atomic.html#chimerax.atomic.structure.AtomicStructure>.
>> 
>> Could you please help?
>> Thanks
>> Yaikhomba
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