[phenixbb] different occupancies for same molecule; optimize final model question

[Pavel Afonine]

Hi Georg,

what you get doesn't look good.

I think you can answers and fix suggestions to this here

" 13 typical occupancy refinement scenarios and available options in 
phenix.refine"
https://www.phenix-online.org/newsletter/CCN_2015_07.pdf

Make sue input occupancies within the residue name&number are the same.

Pavel


On 2/22/16 00:10, Georg Mlynek wrote:
>
>
> On 02/21/2016 11:33 PM, Georg Mlynek wrote:
>> Dear scientific community,
>>
>> 1.
>>
>> if I put in the gui under Modify selections for: Occupancies / simple 
>> occupancy refinement
>>
>> resname SO4
>> resname GOL
>>
>>
>>
>> phenix outputs different occupancies for each of the elements in the 
>> molecule.
>>
>>
>>
>> Is the atom selection syntax wrong or is it a bug?  (Ready set is 
>> also not flagging or correcting this, would be nice is this can be 
>> implemented)
>>
>> 2. I used phenix optimize final model and I wonder why it refines K 
>> anisotropic but not NA and CL.
>> (I would be very nice, if the program could summarize at the end 
>> which settings and strategies were finally used, so this can be added 
>> to the publication: I know it is under development)
>>
>>
>>  adp {
>>       individual {
>>         isotropic = not (element K)
>>         anisotropic = (element K)
>>       }
>>
>>   }
>>     occupancies {
>>       individual = resname NA or resname K or resname CL
>>       remove_selection = None
>>       constrained_group {
>>         selection = None
>>       }
>>
>>
>> I am using ubuntu 15.10
>>
>> phenix version dev-2313-000
>>
>> Many thanks in advance, best regards Georg.
>
>
>
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