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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb