[phenixbb] occupancy refinement

Dalibor Milic dmilic at chem.pmf.hr
Thu Nov 25 10:52:32 PST 2010

```Hi Pavel,

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

is exactly what I want. Nevertheless, this can be done in SHELXL, but I
hoped it could be done in phenix.refine too.

Best regards,
Dalibor

On Čet, studeni 25, 2010 19:26, Pavel Afonine wrote:
>   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
>>
>> ...
>>
>>
>>
>
>

--
Dalibor Milic
Laboratory of General and Inorganic Chemistry
Department of Chemistry
Faculty of Science
University of Zagreb
Horvatovac 102a
HR-10000 Zagreb
Croatia

phone:  +385 1 460 6377
fax:    +385 1 460 6341
e-mail: dmilic at chem.pmf.hr

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