Opened 6 years ago

#2311 assigned defect

Implement "backrub" algorithm for rotamer optimization

Reported by: tic20@… Owned by: Eric Pettersen
Priority: moderate Milestone:
Component: Structure Editing Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

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.

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