On Tue, Feb 10, 2009 at 4:43 PM, Pavel Afonine <PAfonine@lbl.gov> wrote:

Hi Anna,

to find out what's going on I just did the following:

1) I copied the lines below into "answer.pdb" file and I re-set the
occupancies so they all make sense (add up to 1);

2) Using "answer.pdb" file I simulated two datasets: X-ray and neutron:
"data.mtz". What I did is just I computed X-ray and neutron Fcalc, and
called their absolute values as F-obs-xray and F-obs-neutron, and stored
them in "data.mtz".

3) Then I scrambled the model in "answer.pdb" by randomizing the
occupancies of all atoms. This file containing the scrambled models is
called "start.pdb".

4) Finally, I took "data.mtz" and "start.pdb" files and ran joint XN
refinement in phenix.refine. I did only occupancy refinement. As the
refinement result I was expecting to get the PDB file with refined
structure where all the occupancies are exactly the same as in
"answer.pdb". The command I used is:

phenix.refine data.mtz start.pdb params --overwrite

5) Now, open two files "answer.pdb" and "refinement_result_001.pdb", and
voila! All the occupancies are as expected.

All the input and output files discussed above are located here:
http://cci.lbl.gov/~afonine/for_AnneG/

All the above data and files manipulations were done using
"phenix.pdbtools" and "phenix.refine".

Could you reproduce the refinement I just did ("step 4") using your
version of PHENIX ? If not, then please update to the latest PHENIX
(http://www.phenix-online.org/download/) and try again. If not
successful even then, I will send you the latest development version.

Please let me know if you have any questions or problems!

Pavel.

On 2/10/2009 11:04 AM, Anna Gardberg wrote:
> I am doing joint refinement of a perdeuterated protein, and I am
> having a problem with alternate conformations - the deuterium
> occupancies don't match the overall occupancies for their conformation:
>
> ATOM 335 N APRO A 19 13.154 0.897 15.243 0.38
> 8.64 N
> ATOM 336 CA APRO A 19 12.556 0.209 16.391 0.38
> 7.61 C
> ATOM 337 CB APRO A 19 13.743 0.043 17.350 0.38
> 12.47 C
> ATOM 338 CG APRO A 19 14.713 1.102 16.926 0.38
> 9.70 C
> ATOM 339 CD APRO A 19 14.594 1.126 15.443 0.38
> 13.59 C
> ATOM 340 C APRO A 19 11.414 0.974 17.057 0.38
> 13.42 C
> ATOM 341 O APRO A 19 10.559 0.334 17.671 0.38
> 15.65 O
> ATOM 342 DA APRO A 19 12.236 -0.672 16.112 0.48
> 5.78 D
> ATOM 343 DB2APRO A 19 13.454 0.173 18.268 0.43
> 15.49 D
> ATOM 344 DB3APRO A 19 14.128 -0.841 17.229 0.52
> 10.36 D
> ATOM 345 DG2APRO A 19 14.460 1.959 17.300 0.60
> 13.82 D
> ATOM 346 DG3APRO A 19 15.610 0.852 17.197 0.30
> 14.04 D
> ATOM 347 DD2APRO A 19 14.850 1.996 15.097 0.48
> 12.84 D
> ATOM 348 DD3APRO A 19 15.119 0.413 15.046 0.40
> 8.63 D
> ATOM 349 N BPRO A 19 13.163 0.886 15.240 0.62
> 8.58 N
> ATOM 350 CA BPRO A 19 12.606 0.252 16.438 0.62
> 7.70 C
> ATOM 351 CB BPRO A 19 13.777 0.307 17.423 0.62
> 11.89 C
> ATOM 352 CG BPRO A 19 14.973 0.224 16.548 0.62
> 11.13 C
> ATOM 353 CD BPRO A 19 14.616 1.094 15.375 0.62
> 13.76 C
> ATOM 354 C BPRO A 19 11.399 0.972 17.012 0.62
> 13.34 C
> ATOM 355 O BPRO A 19 10.491 0.304 17.514 0.62
> 15.31 O
> ATOM 356 DA BPRO A 19 12.371 -0.680 16.253 0.23
> 7.26 D
> ATOM 357 DB2BPRO A 19 13.760 1.148 17.905 0.72
> 12.42 D
> ATOM 358 DB3BPRO A 19 13.734 -0.446 18.034 0.19
> 14.30 D
> ATOM 359 DG2BPRO A 19 15.759 0.552 17.012 0.87
> 14.63 D
> ATOM 360 DG3BPRO A 19 15.094 -0.695 16.264 0.40
> 9.68 D
> ATOM 361 DD2BPRO A 19 14.807 2.022 15.580 0.43
> 11.93 D
> ATOM 362 DD3BPRO A 19 15.083 0.798 14.578 0.31
> 8.63 D
>
> I am using these refinement options:
> refine {
> strategy = *individual_sites *rigid_body *individual_adp group_adp
> tls \
> *occupancies group_anomalous
> sites {
> individual = None
> rigid_body = None
> }
> occupancies {
> individual = None
> remove_selection = None
> constrained_group {
> selection = None
> }
> }
> }
>
> and
> hydrogens {
> refine = *individual riding
> refine_adp = one_b_per_residue one_b_per_molecule *individual
> refine_occupancies = one_q_per_residue *one_q_per_molecule individual
> contribute_to_f_calc = True
> }
> What refinement options should I be using to keep the D occupancies
> the same as the rest of their conformation? Hope you can help!
>
> Regards,
> Anna

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