[phenixbb] Exclude atoms from refinements

[Pavel Afonine]

Hi Simon,

ok, now I got. Here are the steps to do this:

- set occupancies of atoms to omit to zero:

phenix.pdbtools model.pdb occupancies.set=0 selection="chain A and 
resseq 1:20"

- run phenix.refine with the new PDB file. Make sure you tell the mask 
calculation to not set the bulk-solvent mask in omit region by using 
refinement.mask.ignore_zero_occupancy_atoms=False

Pavel

On 4/16/13 2:17 PM, Simon Kolstoe wrote:
> 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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