[phenixbb] Exclude atoms from refinements

Pavel Afonine pafonine at lbl.gov
Tue Apr 16 10:24:05 PDT 2013

Hi Simon,

based on how far you can stretch your imagination "exclude some atoms 
from refinement " may be something broad:

- do you want to exclude selected atoms from coordinate? occupancy? 
B-factor? ...etc. refinement?
- do you want these atoms to be excluded from bulk-solvent mask 
calculation too (or should they still contribute to the solvent mask)?
- should they still be included into geometry term calculation (so, for 
example, the other atoms are aware of their presence).
.. list of possibilities is long.

So could you please specify more precisely how you want to exclude 
selected atoms (what they still should and should not contribute to)?


On 4/16/13 9:36 AM, Simon Kolstoe wrote:
> Hi,
> I want to exclude some atoms from refinement altogether in phenix.refine. Googling this I came up with the following link:
> http://phenix-online.org/pipermail/phenixbb/2011-December/018020.html
> however was wondering how you implement this sort of thing in the GUI?
> Thanks,
> Simon

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