-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear all,
I am surprised by the discussion about "chiraliy" of an utterly centrosymmetric molecule. Shouldn't the four Oxygen atoms be at least from a QM point-of-view to indistinguishable? What reason is there to maintain a certain 'order' in the human-induced numbering scheme? Cheers, Tim On 07/13/12 00:22, Dale Tronrud wrote: > While this change has made your symptom go away it is stretching it > a bit to call this a "fix". You have not corrected the root > problem that the names you have given your atoms do not match the > convention which is being applied for SO4 groups. Changing the cif > means that you don't have to worry about it, but people who study > such details will be forced to deal with the incorrect labels of > your model in the future. > > Wouldn't it just be easier to swap the names of two oxygen atoms in > each SO4, leaving the cif alone? Your difficulties will go away > and people using your model in the future will also have a simpler > life. > > This labeling problem is not new. The fight to standardize the > labeling of the methyl groups in Valine and Leucine was raging in > the 1980's. Standardizing the labels on the PO4 groups in DNA/RNA > was much more recent. It helps everyone when you know you can > overlay two models and have a logical solution without a "rotation > matrix" with a determinate of -1. > > Besides, you will continue to be bitten by this problem as you use > other programs, until you actually swap some labels. > > Dale Tronrud > > On 07/12/12 15:00, Joel Tyndall wrote: >> 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 > - -- - -- 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/ iD8DBQFP/+M0UxlJ7aRr7hoRAvcqAJ9nuBmSmc2qVyMf17T76stvbqmfEQCfQIDo v9xoSL/c7LGAKFe3B5Rk9Zc= =PSch -----END PGP SIGNATURE-----
