Hi Eric, I realize this is an old thread, but I have the same request as Chase. While I understand your hesitation in implementing bond orders to some extent, omitting them can lead to information loss in certain cases. For example, ligand files in SDF format require bond order data, but when loaded into ChimeraX, this information is missing. Would you consider displaying double and triple bonds when structure files explicitly include this information, such as in SDF, DMS, or MAE formats? If this is not feasible, could the Bond object at least retain bond order information? This would be particularly useful when writing a new SDF file, as missing bond order data could be problematic (perhaps this is one reason why SDF file writing isn't currently supported?). The only visualization software I’m aware of that properly handles bond order information is PyMOL. You might find useful implementation ideas there. Thank you! Best, Siyoung

Siyoung, I did make a bundle that can parse and save SDF files, but I probably won't be uploading it to the toolshed any time soon. I don't really have the time to support it or develop it much further, but hopefully it can help as an intermediate solution. This bundle was just for helping with the Ess/Fleming groups' ORA (organic reaction animation) project. The trajectories shown on the website (https://webora.chem.byu.edu/) or iPhone app (iORA) are stored as SDF files, and we found that automated ways to set the bond order often struggled because of the vibrations during the trajectory. This bundle was really just for making sure we can set the correct bond order in these trajectories, rather than viewing bond order data in ChimeraX. I pretty much just work with small molecule stuff, so I can't promise it will work well for larger biomolecules. Different bond orders are represented using different pseudobond groups. There's some mouse modes for setting the bond orders, where you just click on one atom and then another. There's also a 'guessBondOrders' command that will replace all bonds with pseudobonds based on the distance between atoms. The code for the bundle is here: https://github.com/ajs99778/ChimeraX_ora_stuff . You will have to compile and install the bundle manually. That process is basically just running "devel install /path/to/ChimeraX_ora_stuff" and restarting ChimeraX. Best, Tony On Tue, Feb 4, 2025 at 2:49 PM Eric Pettersen via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:

Hi Siyoung, Well, we do have a tentative plan for implementation, but it's competing with many other implementation priorities so it's still pretty much in the don't-hold-your-breath category. I will add you to the ticket we have open for its implementation, so you will be notified if/when something happens.

--Eric

Eric Pettersen UCSF Computer Graphics Lab

...

On Feb 3, 2025, at 2:50 PM, kkssy141--- via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:

Hi Eric,

I realize this is an old thread, but I have the same request as Chase. While I understand your hesitation in implementing bond orders to some extent, omitting them can lead to information loss in certain cases. For example, ligand files in SDF format require bond order data, but when loaded into ChimeraX, this information is missing.

Would you consider displaying double and triple bonds when structure files explicitly include this information, such as in SDF, DMS, or MAE formats? If this is not feasible, could the Bond object at least retain bond order information? This would be particularly useful when writing a new SDF file, as missing bond order data could be problematic (perhaps this is one reason why SDF file writing isn't currently supported?).

The only visualization software I’m aware of that properly handles bond order information is PyMOL. You might find useful implementation ideas there.

Thank you! Best, Siyoung _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

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Hi Chase, It’s principally because ChimeraX has to work with structures lacking explicit hydrogens, and so while it knows the valence of each atom. it doesn’t necessarily know the order of a particular bond due to tautomerism. Also, some bonds may have a non-integral order, e.g. aromatic ring bonds or carboxylates. It can also be tricky to orient the multiple lines, e.g. you may want to orient the double/triple bonds orthogonal to the view direction whereas you would want non-integral bonds to lie in the relevant plane, unless there isn’t one (e.g. phosphates)! Anyway, it’s kind of a headache, which is why we haven’t done anything about it so far. Certainly something could be done, at least for fully protonated structures, but ChimeraX lacks so many features that we do know how to implement and implement well that we haven’t been motivated to add ones where we’re not even sure what we would do… —Eric Eric Pettersen UCSF Computer Graphics Lab

On Nov 28, 2019, at 6:35 AM, Smith, Chase <chase.smith@mcphs.edu> wrote:

Dear ChimeraX,

I was just wondering why there is no way to represent a double or triple bond in either the ligands or the protein amino acids when viewing as a Stick or Ball-and-Stick representation? I sometimes use Chimera or ChimeraX to make visuals for my lectures, and the students often have difficulty in understanding due to the absence of the multiple bonds. I would love to have the ability to represent the double or triple bonds with multiple lines between the atoms.

Thank you, Chase Smith

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