Hi, Pavel.

Thanks for the quick reply. I downloaded the files, and I got the result you predicted - all the occupancies looked neat and tidy as expected. Since you used those nice occupancies to generate perfect data, which was then refined against, that's what one would expect, right? So I am still left with the issue of the occupancies going nuts in my real refinement. Or am I missing something?

Regards,
Anna


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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