What of course also could have happened, is that the Bfactor restraints
are too tight, forcing, too low Bfactors for the flexible side chain.
Especially after rotatable bonds, Bfactors can increase much more
sharply than many of the older parameter files would allow. In this
case, reducing these restraints would solve the problem.
Herman
________________________________
From: CCP4 bulletin board [mailto:[email protected]] On
Behalf Of [email protected]
Sent: Tuesday, November 20, 2012 9:14 AM
To: [email protected]
Subject: Re: [ccp4bb] occupancy vs. Bfactors
Hi Robby and Grant,
Here I must second Pavel. As Grant just discovered, modern
refinement programs have improved so much, that they will no longer
allow to fudge a low occupancy (sharper but less density) with a high
Bfactor (broader and more density), especially at higher resolutions. In
this case, I would scroll down the contour level and look for
alternative conformations. Even if you don't find any, the most correct
approach in my view would still be to lower the occupancy, although I am
personnally too lazy to do this.
My two cents,
Herman
________________________________
From: CCP4 bulletin board [mailto:[email protected]]
On Behalf Of Robbie Joosten
Sent: Tuesday, November 20, 2012 6:46 AM
To: [email protected]
Subject: Re: [ccp4bb] occupancy vs. Bfactors
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: [email protected]
Subject: [ccp4bb] occupancy vs. Bfactors
To: [email protected]
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
