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:CCP4BB@JISCMAIL.AC.UK] On
Behalf Of Robbie Joosten
Sent: Tuesday, November 20, 2012 6:46 AM
To: CCP4BB@JISCMAIL.AC.UK
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: gdmi...@students.latrobe.edu.au
Subject: [ccp4bb] occupancy vs. Bfactors
To: CCP4BB@JISCMAIL.AC.UK
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
