[phenixbb] occupancy refinement
Pavel Afonine
PAfonine at lbl.gov
Wed Jan 27 07:40:24 PST 2010
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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>>
>
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