[phenixbb] Constrained occ refinement -- sum not equal 1

Pavel Afonine PAfonine at lbl.gov
Tue Feb 10 13:43:21 PST 2009


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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