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Opened 3 years ago
Last modified 3 years ago
#8391 assigned enhancement
Make AlphaFold Coloring CA-distance coloring work for any two aligned structures
| Reported by: | Tom Goddard | Owned by: | Tom Goddard |
|---|---|---|---|
| Priority: | moderate | Milestone: | |
| Component: | Structure Comparison | Version: | |
| Keywords: | Cc: | Eric Pettersen, Elaine Meng | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
Two comments on a YouTube ChimeraX video that shows AlphaFold Coloring, Nicole and Jethro Sims, wanted to use the coloring of residue pairs that are further away than 3 Angstroms on two aligned structures where that were not aligned by the AlphaFold tool. They were confused that it didn't work in that case.
https://www.youtube.com/watch?v=W6KsBfNwDgs&lc=UgzkHq8vN0ZP9DDz77V4AaABAg
That would be a generally useful tool, unrelated to AlphaFold. Currently AlphaFold adds those CA pair distances as a residue attribute after it runs MatchMaker. It might be nice if MatchMaker itself did this and a tool could use it, and of course a simple color by attribute command could use it (although hard for users to discover that).
Change History (3)
comment:1 by , 3 years ago
| Cc: | added |
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follow-up: 2 comment:2 by , 3 years ago
I guess computing RMSD is a side-effect of doing an alignment with for instance the align command, so I'm not sure that is the safest place to put the calculation. I'm also not sure where a GUI interface to do this would be shown. I made a ticket for this because it sounded like something that would be useful to many people, but I have not thought about the details -- just made a ticket so as not to forget it.
Perhaps the rmsd command should do this, so that the attribute could be generated no matter what method was used to align the structures. Then maybe MatchMaker could leverage that.