Hi Grant,
This is part of the recurring side chain
discussion. There is no consensus in the community about what the optimal
approach is.
In your current approach you are adding a model parameter
(occupancy) to improve the fit with the experimental data (remove negative
difference density). You should ask yourself whether you really need to add
that parameter. Are you not overfitting? Is there any clear evidence that
the atoms are not always there?
The alternative model you propose (full
occupancy, high B) has fewer parameters and explains more of the strucure
(you account for all atoms the protein has, prior knowledge). This model
probably also better reflects the uncertainty of the coordinates of the side
chains involved. If your B-factor restraints are not too tight, the
difference densitty should also disappear (equal explanation of the
experimental data). To me that would be a better
model.
HTH,
Robbie
Date: Mon, 19 Nov 2012 23:36:56 +0000
From:
[log in to unmask]Subject: [ccp4bb] occupancy vs.
Bfactors
To:
[log in to unmask]
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