Hi all, Thanks very much to all who responded so quickly. The fix is a one liner in the SO4.cif file (last line)
SO4 chir_01 S O1 O2 O3 both which I believe is now in the 6.3.0 release. Interestingly the chirality parameters were not in the SO4.cif file in 6.1.3 but then appeared in 6.2.0. Once again I'm very happy to get to the bottom of this and get it fixed. I do wonder if it had become over parametrised. Cheers Joel -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Robbie Joosten Sent: Thursday, 12 July 2012 12:16 a.m. To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Chiral volume outliers SO4 Hi Ian, > > @Ian: You'd be surprised how well Refmac can flatten sulfates if you > > have a chiral volume outlier (see Figure 1d in Acta Cryst. D68: > > 484-496 > (2012)). > But this is only because the 'negative' volume sign was erroneously > used in > the chiral restraint instead of 'both' (or better still IMO no chiral restraint at > all), right? If so I don't find it surprising at all that Refmac > tried to flip the > sulphate and ended up flattening it. > Seems to be a good illustration of the GIGO (garbage in - garbage > out) principle. Just because the garbage input in this case is in the official > CCP4 distribution and not (as is of course more commonly the > case) perpetrated by the user doesn't make it any less garbage. The problem is that in the creation of chiral volume targets chemically equivalent (groups of) atoms are not recognized as such. So any new or recreated restraint files will have either 'positiv' or 'negativ' and the problem starts all over again. That is why it is better to stay consistent and choose one chirality (the same one as in the 'ideal' coordinates in the PDB ligand descriptions). This will also make it easier compare ligands after aligning them (this applies to ligands more complex than sulfate). Obviously, users should not be forced to deal with these things. Programs like Refmac and COOT should fix chiral volume inversions for the user, because it is only relevant inside the computer. That is the idea of chiron, just fix these 'problems' automatically by swapping equivalent atoms whenever Refmac gives a chiral volume inversion warning. It should make life a bit easier. > The point I was making is that in this and similar cases you don't > need a chiral > restraint at all: surely 4 bond lengths and 6 bond angles define the chiral > volume pretty well already? Or are there cases where without a chiral > restraint the refinement still tries to flip the chirality (I would > fine that hard to > believe). I agree with you for sulfate, and also for phosphate ;). I don't know what happens in other compounds at poor resolution, when bond and angle targets (and their SDs) are not equivalent. I guess that some angle might 'give way' before others. That is something that should be tested. I have a growing list of chiral centers that have this problem if you are interested. Cheers, Robbie
