[phenixbb] occupancy refinement

[Pavel Afonine]

Hi Marco and Christian,

another trick that I think will work is to assign a non-blanc altloc 
identifier to each SO4 ion. For example:

HETATM 5269  S  ASO4   601      88.394   7.885  58.375  1.00 
26.69           S
HETATM 5270  O1 ASO4   601      88.709   6.482  58.612  1.00 
26.69           O
HETATM 5271  O2 ASO4   601      88.383   8.143  56.832  1.00 
26.69           O
HETATM 5272  O3 ASO4   601      89.311   8.886  58.913  1.00 
26.69           O
HETATM 5273  O4 ASO4   601      87.037   8.083  58.916  1.00 
26.69           O
HETATM 5274  S  ASO4   602     123.263  -1.833  44.610  1.00 
41.54           S
HETATM 5275  O1 ASO4   602     123.408  -1.546  46.092  1.00 
41.54           O
HETATM 5276  O2 ASO4   602     124.616  -2.116  44.068  1.00 
41.54           O
HETATM 5277  O3 ASO4   602     122.687  -0.633  43.944  1.00 
41.54           O
HETATM 5278  O4 ASO4   602     122.349  -3.008  44.466  1.00 
41.54           O

so one occupancy factor will be refined per each ion, and it will be 
constrained between 0 and 1.0.

Pavel.


On 1/27/10 1:14 AM, Marco Bellinzoni wrote:
> Hi Christian,
>
> all you have to do is to define each sulfate as a constrained group 
> for occupancy refinement, like this:
>
> constrained_group {
>        selection = "chain C and resid x"
>      }
>      constrained_group {
>        selection = "chain C and resid y"
>      }
>
> where resid is simply the residue number. The occupancy of all atoms 
> that belong to the same constrained group will be refined to the same 
> value.
>
> Best wishes,
> Marco
>
> Christian Roth wrote:
>> Dear all,
>> I refine a structure of a protein to 1.4 A and found a few SO4-Ions.  
>> I tried to refine this sulfurs and some of these seems to be not 
>> fully occupied, as the negative difference density suggest. I tried 
>> to refine the occupancy of the sulfate ions to get an idea how strong 
>> the different binding sites might be occupied. All sulfate ions are 
>> in Chain C of my pdb. I tried to refine the occupancy individually 
>> using refine.occupancy.individual SO4 but this lead to different 
>> occupnacies for every atom for every atom and theix cant be the case 
>> for sure.  Then I tried and group occupancy  with resname=SO4 but now 
>> every sulfate ion has the same occupancy, which is indicated from my 
>> previous refinements  also not the case, because two ions have no 
>> negative difference density. At the momentI can not figure out how I 
>> should combine the keywords for the individual occupancy refinement 
>> of the different sulfate ions. In my structure. Should I define for 
>> every ion a different chain or how I could overcome this problem?
>> I would be very happy if anyone has a idea to sove this problem or 
>> tell me what keyword I misunderstood in the documentation.
>>
>> Best regards
>> Christian
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>