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Dear users, I tried giving occupancy of 0.65 and 0.6 respectively for all atoms of the two ligands and refined. Now after refinement, the atoms of ligand does not have negative density but those which did not have negative density previously appear positive. So what do I need to do? under what circumstances does a ligand have different occupancies for different atoms or for a group of atoms. Any such references are very much welcome. Thank you Regards Kavya > Sir, > > Yes it is around ligand. The average B-factor of one of the ligand is > 36.78, of which one of the atom has > occupancy B factor > 0.58 39.37 > 0.56 38.77 > 0.87 37.00 > Three atoms are of same type. > The other ligand's overall Bfactor is 17.64. > occupancy B factor > 1.00 19.29 > 0.64 23.90 > Two atoms are of same type. > > So in the present case should I put the occupancy of 0.56 > for all atoms of ligand-1 and 0.64 for all atoms of ligand-2 > and refine? > > I mean will it be wrong to put different occupancies for different > atoms of same ligand? > > I could not see any alternate densities coming up for those atoms > which did not have densities. But 2FoFc map would appear around these > atoms at 0.7 sigma at the same position where the atoms are present. > > Thank you > Regards > Kavya > >> Hi Kavya, >> >> If I understand you correctly (from title and text), you meant your >> negative >> FoFc was around your ligand, is that right? I wonder if this is a case >> in >> which the ligand has an occupancy below 1, but was modeled as 1, so the >> refinement program had to give it a high B factor to compensate that, >> which >> results in the electron density bleeding into nearby space where there >> should not be so much of it. >> If you want to test this hypothesis, one thing you can try is to set the >> occupancy to 0.25, 0.5,0.75 and so on, and refine a few cycles to see >> what >> happens to the maps. Also, what's the B factor of the ligand, and what's >> the >> B of the nearby protein atoms? The difference between them can also give >> you >> some hint for guessing the ligand's occupancy. Some refinement >> programs(phenix.refine and shelx) can also let you refine the ligand's >> occupancy. >> >> As to the "missing" atoms, that could be caused by alternative >> conformations >> of the ligand - assuming you have already done a thorough refinement. >> >> Zhijie >> >> -------------------------------------------------- >> From: "Kavyashree Manjunath" <[log in to unmask]> >> Sent: Friday, May 24, 2013 12:50 PM >> To: <[log in to unmask]> >> Subject: [ccp4bb] Negative FoFc around ligand >> >>> Dear users, >>> >>> I am using refmac 5.7.0029 for refining a structure (resolution 2.2 >>> Ang) >>> bound to 2 ligands. After MR There is a very clear density of ligands >>> but >>> after refinement, I get negative fofc map near one of the ligand upto 5 >>> sigma. However its 2fofc map covers the whole ligand. Also for the >>> other >>> ligand, I do not see any 2fofc density (at 3 sigma) for 2 atoms, >>> without >>> these atoms the ligand is unrealistic. But the density comes up around >>> these at around 0.7 sigma. >>> Overall completeness is 99.9% >>> Rmerge 7.5% >>> >>> What else I need to check in the data. Kindly provide some suggestions. >>> >>> Thanking you >>> Regards >>> Kavya >>> >>> >>> >>> >>> >>> -- >>> This message has been scanned for viruses and >>> dangerous content by MailScanner, and is >>> believed to be clean. >> >> >> -- >> This message has been scanned for viruses and >> dangerous content by MailScanner, and is >> believed to be clean. >> >> > > > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.