occupancy refinement

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Re: [phenixbb] occupancy refinement

Dalibor Milic

25 Nov 2010 25 Nov '10

6:08 p.m.

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 ... -- Dalibor Milic, Dr. Sc. 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: [email protected]

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Pavel Afonine

25 Nov 25 Nov

6:26 p.m.

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

...

Dalibor Milic

6:52 p.m.

Hi Pavel, thank you for your prompt answer. You understood me correctly:

...

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.

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

...

-- 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: [email protected]

Pavel Afonine

9:04 p.m.

...

thank you for your prompt answer. You understood me correctly:

...
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.

Ok, this is exactly what phenix.refine does automatically. I said it in previous email, and this is what is written in the documentation: http://www.phenix-online.org/documentation/refinement.htm#anch20 All the best! Pavel.

Nathaniel Echols

7:08 p.m.

On Thu, Nov 25, 2010 at 10:26 AM, Pavel Afonine wrote:

...

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.

Wait, now I'm confused too - isn't this the entire point of the constrained_group setting? For example, the parameters below: refinement.refine.occupancies.constrained_group { selection = "chain A and resseq 30" selection = "chain A and resseq 451" } If both selections have alternate conformers A and B, and the occupancies for A and B are both 0.5, what would phenix.refine do? -Nat

Pavel Afonine

9:09 p.m.

Hi Nat, the way it's implemented currently: you can't add constraints on top of another constraints. I'm not aware of any existing program that can do it, although technically it's easy to implement. However, Dalibor can do what he wants (if I understand two previous emails correctly). In fact, phenix.refine will do it automatically, so there is no need to even do anything special. Pavel. On 11/25/10 11:08 AM, Nathaniel Echols wrote:

...

On Thu, Nov 25, 2010 at 10:26 AM, Pavel Afonine mailto:[email protected]> wrote:

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.

Wait, now I'm confused too - isn't this the entire point of the constrained_group setting? For example, the parameters below:

refinement.refine.occupancies.constrained_group { selection = "chain A and resseq 30" selection = "chain A and resseq 451" }

If both selections have alternate conformers A and B, and the occupancies for A and B are both 0.5, what would phenix.refine do?

-Nat

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Dalibor Milic

10:05 p.m.

On Čet, studeni 25, 2010 20:08, Nathaniel Echols wrote:

...

On Thu, Nov 25, 2010 at 10:26 AM, Pavel Afonine wrote:

...
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.

Wait, now I'm confused too - isn't this the entire point of the constrained_group setting? For example, the parameters below:

refinement.refine.occupancies.constrained_group { selection = "chain A and resseq 30" selection = "chain A and resseq 451" }

If both selections have alternate conformers A and B, and the occupancies for A and B are both 0.5, what would phenix.refine do?

I tried: refinement.refine.occupancies.constrained_group { selection = "(chain A and resseq 30) or (chain A and resseq 451)" } and got the same occupancy for both altLoc identifiers, i.e. occupancy(AGLU A 30) = occupancy(BGLU A 30) = occupancy(AALA A 451) = occupancy(BALA A 451) and that is not what I wanted to get. Was I doing something wrong? Regards, Dalibor -- 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: [email protected]

Pavel Afonine

10:29 p.m.

Hi Dilabor,

...

I tried:

refinement.refine.occupancies.constrained_group { selection = "(chain A and resseq 30) or (chain A and resseq 451)" }

this means there will be one occupancy refined for all atoms in (chain A and resseq 30) and (chain A and resseq 451). That is all atoms in (chain A and resseq 30) and in (chain A and resseq 451) will have one refined occupancy value between 0 and 1. Could you please send the fraction of your PDB file containing atoms in question and explain occupancies of which atoms should be constrained in refinement and how. I think I'm confused now about what you are trying to achieve... Pavel.

Dalibor Milic

10:34 p.m.

On Čet, studeni 25, 2010 23:29, Pavel Afonine wrote:

...

Could you please send the fraction of your PDB file containing atoms in question and explain occupancies of which atoms should be constrained in refinement and how. I think I'm confused now about what you are trying to achieve...

You have answered my question in your first post. I tried to achieve exactly

...

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

which is currently not available in Phenix (as you wrote). Best regards, Dalibor -- 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: [email protected]

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Dalibor Milic
Nathaniel Echols
Pavel Afonine