As far as I know there are no repulsions restraints applied if the sum
of the atoms occupancies is <=1.0. If one atom is fully occupied. and
another partial then there will be a restraint.
Eleanor
On 12/08/2010 04:45 PM, 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
