[phenixbb] Alternate conformer and HOH clashes

Pavel Afonine pafonine at lbl.gov
Sun Jul 24 15:19:03 PDT 2011

Hi Yuri,

yes Ralf's suggestion should solve this, otherwise please send the PDB 
file with involved residues and tell how you expect them to behave in 


On 7/23/11 12:04 PM, Yuri wrote:
> Dear All,
> I am having trouble refining multiple conformers that would clash into 
> a neighbouring side chain that also has an alternate conformer.
> An attempt to clarify:
> Lets say a Tyr residue has conformation A1, but also moves into a 
> position B1.
> In postition B, its side chain would clash into a neighbour Phe A2. 
> However this Phe has another conformation B2.
> Bottom line, B1 and B2 would not clash, neither would A1 and A2. Any 
> other combo (A1 B2, etc...) would clash.
> When I model it all in I see problems...
> I encounter the same situation with partially occupied HOHs.
> Whats the best way to deal with this
> Thank you

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