Opened 7 years ago
Last modified 7 years ago
#1245 assigned enhancement
Fragment-based model building in density
Reported by: | Owned by: | Tom Goddard | |
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Priority: | moderate | Milestone: | |
Component: | Structure Editing | Version: | |
Keywords: | Cc: | Tristan Croll | |
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
Would like to be able to find short peptide fragments from all structures at the PDB for fitting into x-ray and cryoEM density for building new models. Fragment would match the sequence as well as possible and might further be constrained to match the density with best results presented to the user to examine and choose one as a starting point for further refinement. This kind of building is available in Coot. The algorithmic code to search the PDB structures could perhaps be obtained with ChimeraX just providing the visualization and user interface.
Change History (5)
comment:1 by , 7 years ago
comment:2 by , 7 years ago
If you want to talk to a local expert on this particular subject, Tom Terwilliger at Los Alamos (from the PHENIX team) is one of the best.
comment:3 by , 7 years ago
Cc: | added |
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comment:4 by , 7 years ago
We are unlikely to have time to work on fragment based building for years. So if you Tristan want it you will have to work on it.
This has been one of the big things on my to-do list for ISOLDE for some time now. I'd be perfectly happy if it were instead a general-purpose tool in ChimeraX itself that I can make use of.