[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.
>
> Thanks for your suggestions,
> 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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