Hi -
A quick note -
We (with Chris Ulens) have seen recently in one case that in a case
MATRIX AUTO would give 'excessive' RMSD, close to 0.030.
Checking the cell based on the projection of RMSDs to the cell axes,
a utility kindly provided by WHATCHECK,
it was suggested that the cell might be off. We changed the cell in
the PDB and MTZ and re-refined.
Now, AUTO gives lower RMSDs. If you think about it for a bit, it does
make sense.
The cells we get, especially since sometimes - and most
unfortunately - speed in processing is seen
as more important than being careful (what? you left the synchrotron
before you processed your data ! Shame!)
one or more cell parameters are often inaccurate and this can show is
RMSDs.
I am sure that now we can have a lively discussion about if we are
"allowed' to change the cell by 0.4 A based on
WHATCHECK output, or we need to re-process or re-measure the data ;-)
I am sure Chris can post numbers if requested - I suspect he reads
ccp4bb from his new headquarters in Belgium.
Tassos
On 13 Sep 2007, at 8:25, Jan Dohnalek wrote:
> Just to add to the outliers in Refmac - careful when some of your
> atoms have zero
> occupancy. The bond restraints are not applied any more to these
> atoms (my feeling) and
> CERTAINLY are NOT CHECKED FOR OUTLIERS by Refmac at the end of the
> refinement.
>
> Jan Dohnalek
>
>
> Eleanor Dodson wrote:
>> No comment on the Auto debate, but the RMSD of bonds is a crude
>> measure unless you check the outliers..
>> You can make REFMAC list these - I think it should do so by
>> default actually..
>> Bad metal distances for instance can distort the number enormously.
>>
>> Eleanor
>>
>> Mark Mayer wrote:
>>> Hello all,
>>>
>>> I believer the suggested matrix weight for running refmac is
>>> 'auto'. I'm at the end of refinment for a data set that I've cut
>>> at 1.59 A, so maps are pretty. Here's the logfile with auto
>>> weighting ...
>>>
>>> NOTE bond rmsds !!!!!!!
>>> REMARK 3 R VALUE (WORKING SET) : .15481
>>> REMARK 3 FREE R VALUE : .18739
>>> REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4387 ; .
>>> 033 ; .022
>>> REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5972 ;
>>> 2.776 ; 1.990
>>>
>>> Am I correct that at this resolution one should aim for bond
>>> rmsds of < 0.02. e.g for a weight of 1.0 the rmsd is 0.017, which
>>> seems more reasonable.
>>>
>>> REMARK 3 R VALUE (WORKING SET) : .16228
>>> REMARK 3 FREE R VALUE : .19032
>>> REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4387 ; .
>>> 017 ; .022
>>> REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5972 ;
>>> 1.689 ; 1.990
>>>
>>> I know this has been discussed many times before, but expert
>>> opinion always appreciated.
>>>
>>> Thanks - Mark
>>>
>>>
>>>
>>
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