[phenixbb] Water/residue alternative conformations

Pavel Afonine PAfonine at lbl.gov
Fri May 29 08:55:58 PDT 2009

Hi Roeland,

could you please send the fragment of PDB file that contains residues 
and waters in question, or just  send the whole PDB? What you are trying 
to do is definitely possible in phenix.refine so I presume there must be 
something obvious (oversight somewhere) that makes it not working as 


On 5/29/09 12:58 AM, Roeland Boer wrote:
> 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.
> ------------------------------------------------------------------------
> ------------------------------------------------------------------------
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20090529/572dae3c/attachment-0003.htm>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: image/jpeg
Size: 15515 bytes
Desc: not available
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20090529/572dae3c/attachment-0001.jpeg>

More information about the phenixbb mailing list