On Tue, May 11, 2010 at 8:07 PM, intekhab alam <faisal...@gmail.com> wrote:
> I solved one structure of a viral RNA polymerase in complex with some > ligands at 2.6 A resolution. The ploymerase structure has 3 monomers in the > asymmetric unit and in all the 3 monomers i found |Fo|-|Fc| as well as > 2Fo|-|Fc| map for the ligand. I tried to model my ligand there and after > putting that some naegative density propped up outside the 2Fo|-|Fc| map and > also the postive density inside the 2Fo|-|Fc| map didnt disappeared > completely at 3 sigma (although it is reduced significantly). I tried > putting metals and other things there but most of the positive density is > gone only when i put my ligand there. Besides these the ligand fits well > only in one of the three chains at 1 sigma while in rest two it is around > 0.8 sigma of |Fo|-|Fc| map. I measured the B factor and findout that the B > and C has higher B facors (33) as compared to A (29). can anyone suggest me > about how to improve or fine tune my map around the ligand so that i can get > rid of this positive and negative density (i already have tried different > binding modes. > Try refining the occupancy of the individual ligands - they might just be poorly ordered, but it's not uncommon to have partial binding. I don't know if Refmac does this, but SHELXL, CNS, or phenix.refine will. You could probably approximate this manually too (for instance, just change it to 0.8 for ligands B and C, and recalculate maps), but it's usually less work and more accurate to let the refinement program do it for you. -Nat
