[phenixbb] Constrained occ refinement -- sum not equal 1
Anna Gardberg
anna.s.gardberg at gmail.com
Tue Feb 10 11:04:21 PST 2009
I am doing joint refinement of a perdeuterated protein, and I am having a
problem with alternate conformations - the deuterium occupancies don't match
the overall occupancies for their conformation:
ATOM 335 N APRO A 19 13.154 0.897 15.243 0.38 8.64
N
ATOM 336 CA APRO A 19 12.556 0.209 16.391 0.38 7.61
C
ATOM 337 CB APRO A 19 13.743 0.043 17.350 0.38 12.47
C
ATOM 338 CG APRO A 19 14.713 1.102 16.926 0.38 9.70
C
ATOM 339 CD APRO A 19 14.594 1.126 15.443 0.38 13.59
C
ATOM 340 C APRO A 19 11.414 0.974 17.057 0.38 13.42
C
ATOM 341 O APRO A 19 10.559 0.334 17.671 0.38 15.65
O
ATOM 342 DA APRO A 19 12.236 -0.672 16.112 0.48 5.78
D
ATOM 343 DB2APRO A 19 13.454 0.173 18.268 0.43 15.49
D
ATOM 344 DB3APRO A 19 14.128 -0.841 17.229 0.52 10.36
D
ATOM 345 DG2APRO A 19 14.460 1.959 17.300 0.60 13.82
D
ATOM 346 DG3APRO A 19 15.610 0.852 17.197 0.30 14.04
D
ATOM 347 DD2APRO A 19 14.850 1.996 15.097 0.48 12.84
D
ATOM 348 DD3APRO A 19 15.119 0.413 15.046 0.40 8.63
D
ATOM 349 N BPRO A 19 13.163 0.886 15.240 0.62 8.58
N
ATOM 350 CA BPRO A 19 12.606 0.252 16.438 0.62 7.70
C
ATOM 351 CB BPRO A 19 13.777 0.307 17.423 0.62 11.89
C
ATOM 352 CG BPRO A 19 14.973 0.224 16.548 0.62 11.13
C
ATOM 353 CD BPRO A 19 14.616 1.094 15.375 0.62 13.76
C
ATOM 354 C BPRO A 19 11.399 0.972 17.012 0.62 13.34
C
ATOM 355 O BPRO A 19 10.491 0.304 17.514 0.62 15.31
O
ATOM 356 DA BPRO A 19 12.371 -0.680 16.253 0.23 7.26
D
ATOM 357 DB2BPRO A 19 13.760 1.148 17.905 0.72 12.42
D
ATOM 358 DB3BPRO A 19 13.734 -0.446 18.034 0.19 14.30
D
ATOM 359 DG2BPRO A 19 15.759 0.552 17.012 0.87 14.63
D
ATOM 360 DG3BPRO A 19 15.094 -0.695 16.264 0.40 9.68
D
ATOM 361 DD2BPRO A 19 14.807 2.022 15.580 0.43 11.93
D
ATOM 362 DD3BPRO A 19 15.083 0.798 14.578 0.31 8.63
D
I am using these refinement options:
refine {
strategy = *individual_sites *rigid_body *individual_adp group_adp tls \
*occupancies group_anomalous
sites {
individual = None
rigid_body = None
}
occupancies {
individual = None
remove_selection = None
constrained_group {
selection = None
}
}
}
and
hydrogens {
refine = *individual riding
refine_adp = one_b_per_residue one_b_per_molecule *individual
refine_occupancies = one_q_per_residue *one_q_per_molecule individual
contribute_to_f_calc = True
}
What refinement options should I be using to keep the D occupancies the same
as the rest of their conformation? Hope you can help!
Regards,
Anna
2009/2/4 Pavel Afonine <PAfonine at lbl.gov>
> Hi Carsten,
>
> they should definitely add up to 1. If the PDB file contains altloc
> identifiers, then those atoms should be picked up automatically and you
> don't need to specify any selections. For example, make sure you have
> something like this in your PDB file (the starting occupancies can be any):
>
> ATOM 49 N MET A 10 3.832 -11.001 0.570 1.00
> 11.55 N
> ATOM 50 CA AMET A 10 2.523 -10.377 0.709 0.70
> 12.44 C
> ATOM 51 CA BMET A 10 2.574 -10.279 0.718 0.30
> 12.42 C
> ATOM 54 CB AMET A 10 2.580 -9.129 1.601 0.70
> 14.67 C
> ATOM 55 CB BMET A 10 2.822 -8.921 1.394 0.30
> 13.99 C
> ATOM 60 CG AMET A 10 1.245 -8.462 1.951 0.70
> 18.00 C
> ATOM 61 CG BMET A 10 1.545 -8.166 1.727 0.30
> 17.90 C
> ATOM 66 SD AMET A 10 0.659 -7.204 0.780 0.70
> 19.47 S
> ATOM 67 SD BMET A 10 1.792 -6.615 2.600 0.30
> 26.45 S
> ATOM 68 CE AMET A 10 1.520 -5.730 1.337 0.70
> 20.21 C
> ATOM 69 CE BMET A 10 2.371 -5.566 1.271 0.30
> 26.12 C
> ATOM 76 C MET A 10 2.021 -10.028 -0.671 1.00
> 10.57 C
> ATOM 77 O MET A 10 2.780 -9.724 -1.578 1.00
> 11.30 O
>
> and then everything should be OK.
> Unfortunately, I can't tell much about the selections you use without
> looking at the PDB file, so in your case I would just try the above
> suggestion.
>
> Pavel.
>
>
>
> On 2/4/2009 12:15 PM, Schubert, Carsten [PRDUS] wrote:
>
> Hi,
>
> I am trying to sort out some issues with the constrained occupancy refinement in phenix 1.4.3. The structure I am working on is fairly high resolution ~1.4A and it looks as if a couple of the alternative conformations would benefit from occupancy refinement, no hydrogens are present yet.
>
> I defined the constrained groups like this:
>
> occupancies {
> individual = None
> remove_selection = None
> constrained_group {
> selection = chain A and resid 66 and altid A
> selection = chain A and resid 66 and altid B
> }
> ....
>
> I expected that the sum of occupancies would be restrained to 1, which they should according to the manual, but the refinement gives me occupancies of 0.7 for altid A and 0.34 for altid B, starting values were both 0.5. Similar discrepancies were also present in other groups, like 0.5 A, 0.37 B etc. The latter is the largest deviation from 1 I have seen in thus far. The alternate conformations were generated in coot, by splitting at the CA position.
>
> Is this a rounding error I just have to contend with or is there some other parameter I need to tweak?
>
> Cheers,
>
> Carsten
>
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