Opened 7 years ago

Last modified 7 years ago

#1245 assigned enhancement

Fragment-based model building in density

Reported by: eustermann@… Owned by: Tom Goddard
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 Tristan Croll, 7 years ago

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.

comment:2 by Tristan Croll, 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 Tristan Croll, 7 years ago

Cc: Tristan Croll added

comment:4 by Tom Goddard, 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.

in reply to:  5 ; comment:5 by tic20@…, 7 years ago

No worries. :)

On 2018-08-14 21:11, ChimeraX wrote:

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