# [phenixbb] occupancy refinement

Pavel Afonine pafonine at lbl.gov
Thu Nov 25 10:26:20 PST 2010

```  Hi Dalibor,

did you have a look at " _*Occupancy refinement*_" section in

http://www.phenix-online.org/documentation/refinement.htm

I'm not sure I fully understand the question...
In the example below I see residue #30 has two conformations, A and B,
and they are automatically constrained-refined in phenix.refine and
their sum adds up to 1 (0.52+0.48).
Same for residue #451.

Although I see that occupancy of "AGLU A 30 " = occupancy of "AALA A 451
", it is not guaranteed in refinement, since otherwise that would be a
double-constrained refinement:

constraint #1: occupancy(AGLU A 30) + occupancy(BGLU A 30)=1
constraint #2: occupancy(AGLU A 30) = occupancy(AALA A 451)

which is not currently available.

May be if you could explain some more with more examples we could find a
solution...

Pavel.

On 11/25/10 10:08 AM, Dalibor Milic wrote:
> Dear all!
>
> How to refine occupancies of mutually dependent structural fragments found
> in alternate conformations, but not consecutive in a sequence? E.g. I want
> to refine occupancies of two alternate conformations of residues 30 and
> 451 (see below the corresponding parts of a PDB file). Because of the
> nature of the structural disorder, an occupancy for altLoc A should be
> strictly the same in both fragments - the same is valid for altLoc B. Of
> course, the sum of occupancies for altLoc A and B should add up to 1.
>
> Dalibor Milic
>
> ...
>
> ATOM    376  N  AGLU A  30      23.241  86.975  31.961  0.52 17.13
>    N
> ATOM    377  N  BGLU A  30      18.971  88.677  32.817  0.48  9.05
>    N
> ATOM    378  CA AGLU A  30      23.240  85.507  31.907  0.52 18.89
>    C
> ATOM    379  CA BGLU A  30      19.108  87.234  32.991  0.48 10.00
>    C
> ATOM    380  CB AGLU A  30      21.848  84.946  32.256  0.52 18.78
>    C
> ATOM    381  CB BGLU A  30      17.727  86.562  33.046  0.48 11.01
>    C
> ATOM    382  CG AGLU A  30      21.247  85.562  33.524  0.52 26.38
>    C
> ATOM    383  CG BGLU A  30      16.935  87.037  34.275  0.48 19.26
>    C
> ATOM    384  CD AGLU A  30      20.264  84.659  34.277  0.52 33.36
>    C
> ATOM    385  CD BGLU A  30      15.694  86.223  34.542  0.48 26.60
>    C
> ATOM    386  OE1AGLU A  30      19.437  83.968  33.620  0.52 31.85
>    O
> ATOM    387  OE1BGLU A  30      15.401  85.288  33.762  0.48 33.05
>    O
> ATOM    388  OE2AGLU A  30      20.310  84.678  35.535  0.52 29.12
>    O
> ATOM    389  OE2BGLU A  30      15.007  86.527  35.538  0.48 30.95
>    O
> ATOM    390  C  AGLU A  30      23.750  84.946  30.575  0.52 18.22
>    C
> ATOM    391  C  BGLU A  30      19.976  86.652  31.877  0.48 10.17
>    C
> ATOM    392  O  AGLU A  30      24.319  83.853  30.534  0.52 19.40
>    O
> ATOM    393  O  BGLU A  30      20.621  85.606  32.059  0.48
> 10.67           O
>
> ...
>
> ATOM   4627  N  AALA A 451      31.047  82.837  22.335  0.52 18.30
>    N
> ATOM   4628  N  BALA A 451      29.107  84.432  26.354  0.48  9.81
>    N
> ATOM   4629  CA AALA A 451      31.958  83.502  23.284  0.52 18.73
>    C
> ATOM   4630  CA BALA A 451      29.655  85.424  27.274  0.48  9.73
>    C
> ATOM   4631  CB AALA A 451      32.880  84.486  22.541  0.52 20.38
>    C
> ATOM   4632  CB BALA A 451      30.469  86.474  26.478  0.48 11.60
>    C
> ATOM   4633  C  AALA A 451      31.176  84.206  24.406  0.52 18.79
>    C
> ATOM   4634  C  BALA A 451      28.556  86.128  28.089  0.48  6.84
>    C
> ATOM   4635  O  AALA A 451      30.019  84.593  24.197  0.52 18.25
>    O
> ATOM   4636  O  BALA A 451      27.441  86.357  27.604  0.48  6.81
>    O
>
> ...
>
>
>

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