Dear Sir, Thank you all for your kind advice and clarifications. I will keep the occupancy 1.0 for both the ligands and refine without considering the negative density in this case.
Thanking you Regards Kavya > -----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" <[email protected]> Sent: Friday, >>>> May 24, 2013 12:50 PM To: <[email protected]> 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----- > > -- > 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.
