Dear Garib, Sorry I'm a little confused.
As Eleanor said, Is it true that Refmac doesn't apply vdw restraints if the sum of the atoms occupancies is <= 1? > If you want to deal with translational disorder (e.g. you have a modulated > crystal then there is another way. In my data, there are crystallographic 4-fold axis on c-axis (P4 21 2) and pseudo-translation vector (0.1, 0.1, 0.5), which is indicated by native patterson peak with 22% height of the origin. I can see very clear density at certain position around the 4-fold axis. And around the shifted position (+0.1, +0.1, +0.5), there's definitely the same density but they are superposed with their symmetry mates -- I think they are statically (packing) disordered. Is my case "translational disorder" as you said? If so, how can I solve it? Yours truly, K. Yamashita 2010/12/9 Garib N Murshudov <ga...@ysbl.york.ac.uk>: > 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 > >
