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Opened 4 years ago
Last modified 4 years ago
#4764 assigned enhancement
Visualize missing parts of an atomic model
| Reported by: | Tom Goddard | Owned by: | Tom Goddard |
|---|---|---|---|
| Priority: | moderate | Milestone: | |
| Component: | Structure Analysis | Version: | |
| Keywords: | Cc: | pett, Elaine Meng | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
It would be pretty nice to have a toolbar button that shows all the stuff missing from an atomic structure by placing colored balls. Missing side chain atoms could have one ball at the tip of the residue with size based on number of missing atoms. Missing loops could show a horseshoe of balls joining the two ends, one ball per missing residue so the size of the missing loop would be evident. Missing N and C termini could extend a straight line of balls (one per missing residue) and the last observed residues extending outward. Each of these 4 types of missing structure could be a different color for clarity. Press the toolbar button again and maybe they all go away.
I made a related example that shows missing side chain atoms on the ChimeraX Recipes web site using a 3A cryoEM structure.
https://rbvi.github.io/chimerax-recipes/sidechains/sidechains.html
That example tried to place missing side chain atoms which is hard to do well. The idea in this ticket is to make just a cartoon depiction (taking at most seconds) for surveying new structures.
I've thought quite a few times about marking missing sidechains like this for ISOLDE's purposes - without such an indicator it's impossible to tell at a glance whether a residue is *truly* alanine or a truncation of a larger sidechain. So far haven't had the time to actually do it... but would be really great to have it available!