[phenixbb] alternate conformation

[Pavel Afonine]

Hi Subhash,

> I am refining a structure with ligand in alternate conformations. I 
> tried giving them A and B, it worked. but I feel that this doesnot 
> make interactions between alternate conformations absolutely zero.

a chain with altloc A does not "see" a chain with altloc B from 
non-bonded interactions point of view. The occupancies of altloc A and 
altloc B are coupled so the sum of occupancies is 1, and all occupancies 
within each altloc are equal.

Normally, if your PDB file has properly defined residues (or whatever 
else) in alternative conformations, then you don't need to do anything - 
they will be refined automatically by default.

> Is there any command in phenix similar to Igroup statement in CNS 
> which can be used for such cases.

Paul or Ralf or someone else who knows hopefully will comment on this.

Pavel.