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Hi Dalibor,<br>
<br>
did you have a look at "
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charset=ISO-8859-1">
<u><b>Occupancy refinement</b></u>" section in <br>
<br>
<a class="moz-txt-link-freetext" href="http://www.phenix-online.org/documentation/refinement.htm">http://www.phenix-online.org/documentation/refinement.htm</a><br>
<br>
I'm not sure I fully understand the question... <br>
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).<br>
Same for residue #451.<br>
<br>
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:<br>
<br>
constraint #1: occupancy(AGLU A 30) + occupancy(BGLU A 30)=1
<br>
constraint #2: occupancy(AGLU A 30) = occupancy(AALA A 451)<br>
<br>
which is not currently available. <br>
<br>
May be if you could explain some more with more examples we could
find a solution...<br>
<br>
Pavel.<br>
<br>
<br>
On 11/25/10 10:08 AM, Dalibor Milic wrote:
<blockquote
cite="mid:4357.193.198.194.199.1290708512.squirrel@webmail.chem.pmf.hr"
type="cite">
<pre wrap="">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
...
</pre>
</blockquote>
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