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Dear James,
your explanation is the background of the strong advice to always
build as much as possible before running the next refinement cycle.
I've seen directories with way more than one hundred runs of refmac
and don't want to know what has been hovered into and out of the model...
Best,
Tim
On 11/21/2012 05:04 AM, James Holton wrote:
>
> Something you want to be very careful with here that appears to
> have not been mentioned yet is "phase bias".
>
> If you have built in a wrong side chain or other entity that is
> not actually there, but still force it to have occupancy=1 and
> reasonable B factors (B factor restraints might do that) and then
> you refine the rest of the molecule to convergence, build in lots
> of waters, etc. it is quite astonishing how much "memory" the
> resulting phases can have for the incorrectly-placed atoms. If you
> simply remove the wrong side chain atoms and then re-calculate the
> map with no refinement, then it is not unexpected that you will see
> "green" difference density for it. This may persist even after a
> few cycles of refinement.
>
> Best thing to do after removing a "questioned" feature is to jiggle
> the rest of the molecule a bit, remove all the waters, and then
> re-refine to convergence. If the difference feature survives such
> a treatment, then it is probably for real. This used to be called
> a "simulated annealing omit map". Something that seems to have
> been lost in a few modern packages.
>
> And yes, "phase bias" can work the other way as well. If you
> really do have a low-occupancy feature, then not modeling it and
> re-refining everything else will result in "negative" phase bias:
> squashing your weak feature into oblivion. Exactly what occupancy
> is required to be resistant to a "simulated annealing omit"
> procedure? That's a good question. However, I am reasonably
> confident that this "critical occupancy" is less than 1.0 And
> probably greater than zero as well.
>
> -James Holton MAD Scientist
>
>
> On 11/20/2012 10:36 AM, GRANT MILLS wrote:
>> Hello all,
>>
>> I'm currently working on a structure which if I stub a certain
>> side chain phenix/coot shows me a large green blob which looks
>> strikingly similar to the side chain, when I put it in and run
>> another refinement the blob turns red.
>>
>> Basically I was just playing around and I changed the occupancy
>> of the side chain and now there are no complaints. But I was
>> thinking, should I haven changed the Bfactors instead? Should I
>> have left well enough alone? If I lower the occupancy manually
>> and do not include alternate confirmations have I introduced
>> modelling bias?
>>
>> Could someone recommend some good articles I could read on
>> exactly how to correctly fix this problem.
>>
>> Thanks, GM
>
>
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
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