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Opened 7 years ago
Closed 7 years ago
#1145 closed enhancement (fixed)
Assign B-factors to added atoms
| Reported by: | Tristan Croll | Owned by: | Tom Goddard |
|---|---|---|---|
| Priority: | moderate | Milestone: | |
| Component: | Structure Editing | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
This applies to AddH and SwapAA at present. It would be great if the added atoms were assigned reasonable B-factors on addition (e.g. the B-factor of the heavy atom for hydrogen addition; the average of the backbone B-factors for swapAA). Crystallographic and high-res cryo-EM refinement are both very sensitive to B-factor, and do best when the starting guesses are reasonably close to reality. For example, adding zero-b-factor hydrogens to the 272 waters in a well-refined 892-residue, 2.1-Angstrom crystal structure increases the R-free by about 4%, and phenix.refine really struggles to bring it back down.
Change History (3)
comment:1 by , 7 years ago
| Status: | assigned → accepted |
|---|
comment:2 by , 7 years ago
| Owner: | changed from to |
|---|---|
| Status: | accepted → assigned |
comment:3 by , 7 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Swapaa mouse mode now sets the side chain b-factors of the new residue to the average of the backbone b-factors of the replaced residue.
I have changed AddH to give the added atoms the same bfactor as their bond partner. SwapAA was implemented by T.G. so I am now reassigning the ticket to him.
--Eric