-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Kavya,
I don't see much sense in having different occupancies within the same molecule (unless one atoms sits on a special position, but then refmac will take care of it). If positive density comes up it's a good sign the ligand really is there. At 2.2A I would not be too surprised some atoms show less density than others (but don't look too much at the map with a sigma level < 1: you are going to see what you want to see). It's difficult to judge without sitting next to you, so my advice is try to model it as good as your knowledge permits, and do take your chemical knowledge into account when doing so! Best, Tim On 05/25/2013 06:55 AM, Kavyashree Manjunath wrote: > 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" <ka...@ssl.serc.iisc.in> Sent: Friday, >>> May 24, 2013 12:50 PM To: <CCP4BB@JISCMAIL.AC.UK> 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. >> > > > - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRoHp0UxlJ7aRr7hoRAti/AJ9PQQE8cgccPFuaWN842qlwkCK8FgCg/BPR 8485l18SMJ4Th5XD0X5be1w= =GfVo -----END PGP SIGNATURE-----
