Need a method to clear atom's anisotropic B-factors

[Tristan Croll]

Not to set the entries to zero, but to clear the Atom.aniso_u field entirely and set Atom.has_aniso_u to False. Anisotropic B-factors are some of the most abused parameters in model refinement, and it's often advantageous to wipe them and start over (or switch to using purely isotropic B-factors). At the moment I can fudge the effect I want by setting all the aniso_u terms to NaN (internally, Clipper treats this as the atom having no anisotropic B-factors) - but that leads to garbage ANISOU records being written to the PDB file on saving.

[Eric Pettersen]

a.aniso_u6 = None

will now clear the aniso_u info.

[tic20@…]

Thank you!

 
 
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY
 

 

[tic20@…]

This isn't quite working as expected.

for a in model.atoms:
     a.aniso_u6 = None

... clears the anisotropic b-factors, but

model.atoms.aniso_u6 = None

... doesn't (instead sets them all to NaN).


On 2019-01-19 00:37, ChimeraX wrote:

[Eric Pettersen]

Okay, this works now for collections too.

--Eric