At the moment there is no way of telling refmac to ignore clashes between symmetry related atoms. Is there any reason you would want to do that? Perhaps there are other ways of solving the problem you would like to solve. I can add a keyword to force to ignore these clashes if there is sufficiently good argument to do so.
If you want to deal with translational disorder (e.g. you have a modulated crystal then there is another way. You just give your molecules and then ask the program to ignore clashes. regards Garib On 8 Dec 2010, at 16:45, Keitaro Yamashita wrote: > Dear Ed, > > These tables were reported by Refmac5: > > Before refinement, > ------------------------------------------------------------------------------- > Restraint type N restraints Rms Delta Av(Sigma) > ..... > VDW repulsions: symmetry: refined_atoms 38 0.232 0.200 > VDW repulsions: symmetry: others 100 0.393 0.200 > HBOND: symmetry: refined_atoms 11 0.229 0.200 > HBOND: symmetry: others 1 0.120 0.200 > ..... > ------------------------------------------------------------------------------- > > After refinement, > > VDW repulsions: symmetry: refined_atoms 27 0.190 0.200 > VDW repulsions: symmetry: others 76 0.262 0.200 > HBOND: symmetry: refined_atoms 13 0.225 0.200 > > > I thought that meant there's vdw repulsion energy among symmetry > related atoms, which I want refmac5 to ignore. > > > K. Yamashita > > 2010/12/9 Ed Pozharski <[email protected]>: >> On Thu, 2010-12-09 at 01:09 +0900, Keitaro Yamashita wrote: >>> When I tried to refine using Refmac5, the output told many vdw >>> repulsions with symmetry mates >> >> What do you mean by that? I had a similar situation recently, and there >> are many records in the log file that say something like this >> >> INFO: link is found (not be used) dist= 1.531 ideal_dist= >> 1.500 >> ch:AA res: 217 GLN at:C .->ch:FF res: 217 GLN >> at:CA . >> >> Note the "not be used" part. AFAIU, these clashes are simply reported >> but ignored in refinement. Perhaps some keyword like "monitor none" >> shall turn these warnings off, but other than making your log-files very >> long it's not a problem. >> >> -- >> "I'd jump in myself, if I weren't so good at whistling." >> Julian, King of Lemurs >>
