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Changes between Initial Version and Version 1 of Ticket #2310

Ticket #2310
- Property Cc Elaine Meng added
- Property Status assigned → accepted

initial	v1
1	1	I can see `swapaa` being really useful for a lot of things (e.g. filling in missing sidechains), but it would be great if it had the option to add hydrogens to the new sidechain (and turn it on by default if there are hydrogens in the starting residue?). Alternatively/equivalently an option to restrict `addh` to a selection of residues, so one could just do e.g. `swapaa sel LYS; addh sel` (which currently works, but is slow for big models since the `addh` selection expands to the entire model).
2
3		A less pressing potential enhancement would be to include the "backrub" algorithm when optimising the rotamer for clashes/fit to density (https://academic.oup.com/bioinformatics/article/24/13/i196/233217). It's quite simple to implement and often makes a big difference, although it still doesn't help in every case (in particular, a 180 degree flip around chi1 of Ile, where you really need a degree of freedom waggling CB ~parallel to the N-C axis to avoid the sidechain staying obstinately out of density). I have a basic version in ISOLDE, although I need to do some more intelligent weighting of density vs. clashes and prior probability before it'll be really useful.