biasmv
Support bond orders
It looks like bond objects only include two atoms and a mid point, and that it is not currently possible to render double, triple or aromatic bonds.
Could bond order please be added to bonds, with appropriate rendering options?
Hi,
thanks for the suggestion.
Having bond order displayed is a good idea. Rendering them is the easy part. The more complex part is to find a good and fast heuristic to determine the bond order. In the past, we have used dictionaries with definitions for each residue that appears in PDB files and used the bond order that was specified in these files. These dictionaries tend to get quite large (a few megabytes), so transferring them to the client side is not a good option, at least not without filtering them and only sending the residue types which actually appear in the structure.
We could store definitions for the most common amino acids, but to me, the bond order for the standard amino acids is the least interesting. Bond order information is most useful for ligands they change from structure to structure :).
What I could suggest: provide a means to render the bond order for the lines and balls and sticks render styles and provide mechanisms to the set the bond order. Then we can experiment with different heuristics, or even add loaders for other sources of bond order information.
Having said that, adding bond orders is certainly a good idea, but I can't make any promises time-wise. Patches in that direction are certainly welcome, so if you are interested in contributing anything in that area, that would be great.
Best, Marco
Hello,
As a common technique - e.g. in PyMol - the atomic distances are used to predict the bond order. As far as I know, It's work quite well and effectively, fast and does not require large libraries.
Cheers, Daniel
