[phenixbb] occupancy refinement

Oganesyan, Vaheh OganesyanV at MedImmune.com
Wed Jan 27 09:38:26 PST 2010

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.


-----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...


Anyway, I was just pointing out an alternative option for group 
occupancy refinement, and thanks for emphasizing the implications for 
geometry restraints.


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