[phenixbb] occupancy refinement

Ed Pozharski epozh001 at umaryland.edu
Wed Jan 27 10:56:24 PST 2010

It did work for me earlier this month


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



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: phenixbb-bounces at phenix-online.org
> [mailto:phenixbb-bounces at phenix-online.org] 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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Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
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Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
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------------------------------   / Lao Tse /

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