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

[Georg Mlynek]

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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