It did work for me earlier this month http://phenix-online.org/pipermail/phenixbb/2010-January/003180.html As for potential pitfalls of this approach mentioned by Marco, Vaheh is absolutely right that only *other* alternate conformers pose danger here. But even if there are alternate conformers nearby, couldn't some of them clash with the ligands because, you know, ligand is not always there? In any event, simple visual inspection should resolve any specific case. Assigned altLoc is a workaround though and it is my understanding that default phenix.refine behavior with respect to partial occupancy ligands will change in the future to more expected single occupancy per residue default: http://phenix-online.org/pipermail/phenixbb/2010-January/003183.html Ed. On Wed, 2010-01-27 at 12:38 -0500, Oganesyan, Vaheh wrote:
But if you want to refine occupancies of SO4 group only then other atoms, i.e. protein atoms, will not have any altloc. So, no danger and Pavel's trick will work.
Vaheh
-----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Pavel Afonine Sent: Wednesday, January 27, 2010 12:33 PM To: PHENIX user mailing list Subject: Re: [phenixbb] occupancy refinement
Hi Marco,
your trick seems to me potentially 'dangerous', though: if you assign an altloc identifier to a whole residue, its atoms won't 'see' any other atom that does have a different altloc identifier because it is like they don't exist at the same time - is this right?
that's true. Although, I don't know what is actually correct... If the occupancy of the whole ion is less than 1.0 that means there are situations (unit cells) where this ion is simply absent at that particular location and therefore there is nothing to "see" for the surrounding atoms.
If so, in principle, a sulfate labelled with an altloc identifier 'A' should not see neighbouring atoms which are labelled as altloc 'B', which may well be the whole side chain of a residue in close contact, modelled in double conformation. That way, no restraints will be applied on close non bonded atoms, etc...
Correct.
Anyway, I was just pointing out an alternative option for group occupancy refinement, and thanks for emphasizing the implications for geometry restraints.
Pavel.
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