[phenixbb] fix rotamers question

Pavel Afonine pafonine at lbl.gov
Tue Oct 19 23:52:08 PDT 2010

  Hi Peter,

general answer about how the whole thing works, see this:



> - How Phenix chooses which rotamers need to be fixed ?

see above.

> - Does Phenix really re-calculate the three maps after correcting each 
> rotamer ? 

no, it happens only after one walk-through the all residues. In future 
this will be optimize to improve memory consumption.

> -Can you please explain how fix_rotamers works together with ncs 
> restraints ?

The whole procedure is not aware of NCS, or, actually, NCS should be 
smarter. This is in our plans to make better.

Also, fix_rotamers may not perform as good as desired at lower 
resolutions. For this case we also have a number of things to work on, 
such as automatically using B-factor sharpened maps, locally-scaled 
maps, etc...


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