[phenixbb] Constrained occ refinement -- sum not equal 1

[Pavel Afonine]

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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>   
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