[chimerax-users] Making new bonds

[Tom Goddard]

Hi Yaikhomba,

  One more hacky way to add a bond, the "marker link" command.  The marker command is intended to place markers on density maps and link them to trace paths.  But it really just makes atoms and bonds.  So to make your disulphide bond between residues 3 and 16:

	marker link :3,16 at SG radius 0.2

This makes bond color yellow instead of matching the atoms, to remedy that:

	color :3,16 at SG halfbond true

You could make an alias to do these two commands

	alias bond marker link $1 radius 0.2 ; color $1 halfbond true

then just use

	bond :3,16 at SG

  Tom


> On Apr 7, 2020, at 4:24 AM, Mutum YAikhombA <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
> _______________________________________________
> ChimeraX-users mailing list
> ChimeraX-users at cgl.ucsf.edu
> Manage subscription:
> http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20200407/fdc09fce/attachment.html>