Using Jalview certainly could be the way to go. As for trying to do this directly in ChimeraX...
I'm looking for a way to combine multiple sequence based selections into one selection but I wasn't able to find a way to do this. The use case is, I have a lot of models that have these two proteins and I would like to use them together for superposition (via align command against Calphas). I would normally refer to them by chain ID, but here these are not consistently assigned so I need to use the sequence for selection.
If you are trying to specify all chains with the exact same sequence as a particular chain, say chain A in model 1, then the selector would be:
//identity="#1/A"
This 'identity' pseudo-attribute isn't restricted to a single sequence. You could use:
//identity="#1/A,B"
to select all chains with the exact same sequence as chains A or B in model 1.
Is it possible to have a named, sequence-based selection that, when called, would perform the selection? This would save a lot of pain when writing scripts for sequence based selections.
You could only use "frozen" selectors (contents determined when the selector is defined, and does not change when additional structures are opened). So you could define an 'ldsa' selector that refers to the sequence LDSA in the structures open at the time it's defined with:
sel seq LDSA ; name frozen ldsa sel
Then 'ldsa' can be used like any other selector,, .e.g. "color ldsa red". You could use the 'alias' command to make it easier to create these selectors, which means you could put the aliases in your startup commands, and use the alias when you need it.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab