[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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