[phenixbb] Water/residue alternative conformations

Roeland Boer rbocri at ibmb.csic.es
Fri May 29 08:44:27 PDT 2009

Dear Mark,

Thanks for the suggestion. I changed the altlocs of the residue and the 
water so that they are consistent (the water molecule replaces alt conf 
B of res 13, which is the lower occupancy alt conf, and makes a H-bond 
with alt conf A of res13) but the water is still pushed away. The 
updated lines used for the occupancy refinement:

      constrained_group {
        selection = chain A and resseq 13 and altloc B
        selection = (chain A and resseq 13 and altloc A) or (resname HOH 
and resseq 1519 and altloc A)

Any help would be greatly appreciated, because I see this happening a 
lot throughout the structure.


Mayer, Mark (NIH/NICHD) [E] escribió:
> Roeland,
> Have you checked that that water altloc should be B and not A?
> i.e. if your water replaces side chain altloc A, then water
> altloc should be B and not A. This works in my lab.
> -----Original Message-----
> From: Roeland Boer [mailto:rbocri at ibmb.csic.es]
> Sent: Fri 5/29/2009 3:58 AM
> To: phenixbb at phenix-online.org
> Subject: [phenixbb] Water/residue alternative conformations
> Dear all,
> I'm refining a 1.45 Ang structure in which I have several residues that
> have alternate conformations. These alternate conformations in some
> cases coincide with additional density that suggests the presence of a
> water molecule, appropriately positioned to make hydrogen bonds with
> near atoms. I have modeled partially occupied waters in these additional
> densities and linked their occupancies with the alternate conformation
> that is not clashing with the water in question. My problem is that
> these partially occupied waters are pushed away by the 'overlapping'
> alternate conformation of the amino acids. I guess there's an antibump
> restraint somewhere? How can I tell phenix that these alternate waters
> are not sterically clashing with the amino acid (since the sum
> occupancies of the water plus alternate conformation is 1)?
> The attached image shows one of those disordered residues after
> refinement. Water 1519 is pushed away from one alt conf (A) of Gln13,
> whereas the density suggests it should be making a hydrogen bond to OE1
> of the altconf B of Gln13.
> I describe the occupancies of the situation in the attached image as below.
> refinement {
>     refine {
>       occupancies {
>          constrained_group {
>           selection = chain A and resseq 13 and altloc A
>           selection = (chain A and resseq 13 and altloc B) or (resname HOH
> and resseq 1519 and altloc A)
>         }
>       }
>     }
> }
> Thanks,
> Roeland Boer.
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