[phenixbb] A few questions
PAfonine at lbl.gov
Wed Feb 6 11:48:18 PST 2008
thanks for the data. I'm looking at your parameters file (test2). In the
strategy = *individual_sites rigid_body *individual_adp group_adp tls \
individual_occupancies *group_occupancies group_anomalous
I see you are using group_occupancies which means that one occupancy per
residue will be refined (unless you provide your own selections to
define the groups). As I mentioned before, group_occupancies does not
use any constraints and it is not aware of alternative conformations.
This is why in the example below the sum of occupancies is not 1.0. I
think this is not what you want to do. I will add the constrains to
group_occupancies option so you get equal occupancies within each
conformer and the sum of occupancies computed for all conformers is 1.0.
Currently, if you choose individual_occupancies then you will get the
constraints, that is the sum of occupancies for "523 SE AMSE A 32" and
"530 SE BMSE A 32" will be one, but the occupancies for atoms within
each conformer will be different, which is, as Paul correctly pointed
out, not 100% right.
I will keep you posted about the progress.
> In that case, then the occ of alt conf's tends to refine to greater than 1:
> ATOM 523 SE AMSE A 32 23.654 11.792 6.216 0.56 14.04 Se
> ATOM 530 SE BMSE A 32 23.570 12.284 6.796 0.46 13.91 Se
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