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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