Thanks for the input. I guess as a relatively transient user I am not appreciating the depth of the problem. However, by at least raising this issue, I'm hoping that the "fight" can be sorted out. Where does my "sulfate" problem stem from? Is it from importing the fragment in COOT? Is it the actual cif file which is read by COOT? As noted, software updates tend to be quicker than we can refine our structures (That albeit is relatively slow on our behalf). I am all for standardisation, but in the long run (at least for me) the sulfate(s) becomes a minor part of the structures.
I'll look at swapping the oxygens in the SO4's.
From: Dale Tronrud [mailto:[log in to unmask]]
Sent: Friday, 13 July 2012 10:22 a.m.
To: Joel Tyndall
Cc: [log in to unmask]
Subject: Re: [ccp4bb] Chiral volume outliers SO4
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.
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.
> -----Original Message-----
> From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
> Robbie Joosten
> Sent: Thursday, 12 July 2012 12:16 a.m.
> To: [log in to unmask]
> 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:
>> But this is only because the 'negative' volume sign was erroneously
>> 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
>> 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
>> restraint at all: surely 4 bond lengths and 6 bond angles define the
>> 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
> 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.