Added trim option to AlphaFold panel

[phil.cruz@…]

Phil would like to be able to turn off trimming when fetching AlphaFold database models from the AlphaFold GUI so that predicted aligned error plots can be used. Currently the AlphaFold model has residues deleted that are not part of the experimental sequence used to fetch it. But currently ChimeraX cannot show predicted aligned error (PAE) on an AlphaFold model with deleted residues. By avoiding trimming, PAE can be used for coloring.

Another and possibly better improvement would be to allow use of PAE on AlphaFold models with deleted residues.

[Tom Goddard]

Done.

I added an option to the AlphaFold user interface "Trim fetched structure to the aligned structure sequence", default True.

This option only applies to the Fetch button of the AlphaFold user interface, not the Search or Predict buttons. Search does a BLAST search and double clicking one of the results in its table aligns it and trims it to the experimental structure. So it would be nice if the trim option worked for Search, but the blast tool has no ability to accept a trim option to say whether to trim when loading an AlphaFold database model (blast could even conceivably support trimming to any aligned model). I made a ticket to see if BLAST search could handle the trim option, #7240. Predict never trims so the trim option is not relevant when using Predict.

[Tom Goddard]

I also made PAE plots work with trimmed AlphaFold models, ticket #7246.