[chimerax-users] Making New Bonds between two molecules in ChimeraX

[Steven Truong]

Dear ChimeraX Admins and Elaine,

Hello, I was wondering if ChimeraX now has a “bond” command.  I saw an inquiry like this in the mailing list archives (https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-April/001029.html), but it seems like bond is still not an official functionality.  When I switched over to Chimera and tried using the “bond” command, I get the error “Cannot form covalent bond joining two molecules,” even though I’ve saved all of the molecules into one PDB file.  Is it because Chimera still sees these two sub-models as un-joinable?  My command looks something like: "bond #0:61.A at ND2 #0.1:1222.X at C1”.

For further context, we are trying to script orienting/bonding residues to glycans.  We’ve been able to figure out aligning and orienting the glycans quite well with the scripts alone (.py scripts), but it seems like we’ll have to find another way to make bonds between the proteins/glycans.  Do you have any suggestions?  Ideally, we’d also keep as much of the pipeline in ChimeraX, but if it’s necessary, we could further pursue the ChimeraX+Chimera route.

Thank you for your help!

Many thanks,
Steven Truong
sdt45 at cam.ac.uk<mailto:sdt45 at cam.ac.uk>
Cambridge University
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