Obviously no refined parameters can ever be completely error-free, it's
just that for the co-ordinates we have very accurate geometric restraints
so that the relative uncertainty in the refined co-ordinates is small (but
try refining co-ordinates without restraints!). For the B factors we don't
ha
Yes, it is and I like the definition of shared “trash bin”. It will have more
physical meaning if we can separate those contributions into separate bins.
Vaheh
From: Pavel Afonine
Sent: Tuesday, July 30, 2024 1:51 PM
To: Oganesyan, Vaheh
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] How hi
Vaheh,
I think coordinates are no different from B factors, occupancies, f', or
f'' in this respect. Coordinates can play their "trash bin" role by
adjusting to the noise at the expense of violated geometry (bonds, angles,
planes, torsions, etc.). As I mentioned in my previous email, their trash
b
**Question:**
After step 11 in my pandda-export folder I have the following files:
File name:
Remarks:
1
ensemble-model.log
2
ensemble-model.pdb
Contains both bound and ground-state
3
ensemble-model-restraints.log
4
ensemble-model-restraints.phenix.params
5
ensemble-model
Your point is taken, Pavel. However, despite resolution, you define coordinate
of the atom as a geometric point with no width. Although coordinates are
“refineable”, they have no capacity for “trash”. Their “trash” still goes into
B-factor “trash bin”. At least this is how I see it.
Thank you.
“That which is not restricted will take its liberties”
(Wayne Hendrickson)
https://www.sciencedirect.com/science/article/pii/S0969212601001873
in turn, apparently from one of the older CCP4 workshops
P.A. Machin, J.W. Campbell, M. Elder (Eds)
Refinement of Protein Structures, SERC Daresbury Labor
>From this perspective, all refinable atomic model parameters can be viewed
as trash bins, with the size of these bins being proportional to the amount
of prior information (restraints) imposed on these parameters. For example,
coordinates have the most restraints and thus are the smallest trash bi
Early in my Crystallography life I was postdoc with Robert Huber in Munich. We
had those gatherings once a week when in very informal way we can ask and
answer questions. I remember my question about B factors: how is it possible to
have high resolution structure and average B-factor of 100A2. I
The reason why phenix.refine allows B factors to grow until they fit the
map is that it uses restraints that do not only require the similarity of B
factors of covalently bonded atoms, but rather the similarity of B factors
of atoms located within a sphere of radius R (around 5Å). This is to
accoun
If it hasn't already been mentioned, I would humbly like to remind everyone
that a high B-factor on an atom causes it to have a small or negligible
contribution to a fourier transform. Therefore, beware that modelling
atoms with high B-factors could be introducing model bias by inserting
atoms tha
How high B factors can go depends on the refinement program you are using.
In fact, my impression is that the division between the "let the B
factors blow up" and "delete the unseen" camps is correlated to their
preferred refinement program. You see, phenix.refine is relatively
aggressive with
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