In refmac you can remove vdw interactions between chains using the following command
It is an example: vdwr exclude between chains A B or between resdues: vdwr exclude between residues first residue 123 chain A second residue 155 chain B Regards Garib On 8 Dec 2010, at 16:09, Keitaro Yamashita wrote: > Dear all, > > I'm refining complex structure against X-ray diffraction data with > packing disorder. > (Some domains overlap with their symmetry mates (4-fold), so their > occupancies are set to 0.25) > > I'd like to know whether refinement programs can exclude any > interaction among symmetry mates from geometric term in target > function. > Can it be done only for specific chains? > > I was thankfully taught phenix.refine could do that with the option > pdb_interpretation.custom_nonbonded_symmetry_exclusion in phenixbb. > > I'd very much like to know whether Refmac5, CNS or other programs can do that. > > (When I tried to refine using Refmac5, the output told many vdw > repulsions with symmetry mates.) > > > Thank you very much in advance, > > K. Yamashita
