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<[log in to unmask]>:
>> 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
>>
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