[phenixbb] Exclude atoms from refinements

[Simon Kolstoe]

Hi Pavel,

I want to make an omit map however whenever I delete my ligand the residues/atoms around the binding site get pulled into the ligand density. So I just want to fix the relevant side-chains/atoms in place whilst doing my simulated annealing step. So exclude from xyz movement is the main thing, occupancy, B-factor, bulk solvent etc. is not as important.

Thanks (and also thanks Nat),

Simon


On 16 Apr 2013, at 18:24, Pavel Afonine wrote:

> 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)?
> 
> Pavel
> 
> 
> 
> 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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