Dear All, Thank you for a solution. Probably this is the Best solution for this problem.
Thank you Regards Kavya > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Dear Antony, > > I agree, modelling entirely separate entities with one occupancy for > all atoms inside make chemically much more sense and it has the > advantage that the refinement program can move e.g. ADP to a slightly > different position than ATP - it is unlikely that the common atoms > between the two molecules are exactly in the same position. > > Best, > Tim > > On 05/25/2013 12:34 PM, Antony Oliver wrote: >> Kavya, >> >> Presumably your enzyme is turning over the ATP? Driving it towards >> ADP? >> >> In that case I suspect that you may have a mixture of ATP and ADP >> (and possibly contaminating AMP). You could either model both ATP >> and ADP, and set relative occupancies of both (add up to 1). Or, >> you could assign different occupancies to the phosphate groups >> alone. I personally think the former is probably the correct >> method? Comments CCP4 community? >> >> Many regards, Antony. >> >> >> On 25 May 2013, at 11:29, <[email protected]> wrote: >> >>> Dear Sir, >>> >>> That is true the ligand is ATP, the occupancy problem comes only >>> for the phosphates. This ATP tends to get cleaved to ADP and AMP >>> in other complexes I got. So in this case do you suggest keeping >>> different occupancies for nucleoside and phosphate groups? I am >>> not aware of any publication with this scenario so I am not sure >>> whether it is right. >>> >>> >>> Thank you Regards Kavya >>> >>>> Dear Kavyashree, >>>> >>>> It is possible that your bound ligand (for which you have >>>> strong electron density) is actually a break-down of the parent >>>> compound? We have seen this a couple of times now. >>>> >>>> Also - are the poorly refining areas (those with negative >>>> density) part of a pendant ring connected by a conformationally >>>> unrestricted bond? These quite often have poor density. >>>> >>>> Hard to judge without seeing the actual density - but >>>> understand why! >>>> >>>> Regards, Antony. >>>> >>>> >>>> Sent from my iPhone >>>> >>>> On 25 May 2013, at 10:40, "Kavyashree Manjunath" >>>> <[email protected]> wrote: >>>> >>>>> 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 >>>>> >>>>> >>>>> >> 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. >> >>>>>> >>>>>> -- 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. >>> >> > > - -- > 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/ > > iD8DBQFRoKi6UxlJ7aRr7hoRApC5AJ4xpCWCzM7rDtZYeHNJNBvh8lsgdQCeIxc7 > 14cm2XkebzvgDH0BsTr4M+o= > =fdnh > -----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.
