OK, I see. I looked at my log-files, and I also have about 30 restraints for for VDW_symm. Then I looked at another structure with no packing issues, and the corresponding numbers is ~90. What I am saying is that the number of restraints that you have appears to be reasonable.
It seems that clashes between partial occupancy atoms that you are worried about are ignored after all. If that is the case, do you have another reason to remove this type of restraint? Ed. On Thu, 2010-12-09 at 01:45 +0900, 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 > > -- "I'd jump in myself, if I weren't so good at whistling." Julian, King of Lemurs
