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
>
