Hi all,
I am trying to get some insight in the accuracy/precision of occupancy
refinements. I have done some 2-state occupancy refinements and have observed
the refinement achieving ~0.25-0.3 occupancy for the minor population. This
population, when observing the electron density maps, had es
Hi Matt,
I believe figure 3 here:
https://www.nature.com/articles/s41467-018-06957-w
is relevant to your question.
Pavel
On Tue, Sep 5, 2023 at 11:32 AM Matt McLeod wrote:
> Hi all,
>
> I am trying to get some insight in the accuracy/precision of occupancy
> refinements. I have done some 2-sta
Well - occupancy refinement is particularly imprecise, and highly
correlated with temperature factors.
Also the population for a surface ARG or LYS may well have more than two
conformations, whereas some internal residue is better defined.
There is also the Q of solvent - dual occupancies will gene
Hi Matt,
this can be done with SHELXL, even at 2-3A resolution. Anomalous data
do help reduce the correlation between B-factor and occupancy
(see e.g. https://doi.org/10.1126/science.1254840 to stick with Pavel's
example)
SHELXL prints the correlation coefficient between occupancy and
b-factor,
Dear Matt,I believe this study we made may well assist your evaluations:-(IUCr) Experience with exchange and archiving of raw data: comparison of data from two diffractometers and four software packages on a series of lysozyme crystalsjournals.iucr.orgBest wishes,John Emeritus Professor John R Hell
Hi,
I should be a bit more specific.
We have many crystal structures to indicate that a loop adopts conformation
A and conformation B, or - the loop can be disordered where the electron
density is washed out. These states are dependent on how we perturb the
system.
We have a series of data, as
I would be tempted to try phenix.ensemble_refinement instead.
Look at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3949522/
or
https://phenix-online.org/phenixwebsite_static/mainsite/files/presentations/ensemble_refinement_burnley_at_al_10DEC2012.pdf
or https://elifesciences.org/articles/00311
T
Low tech but simple.
Exclude both conformers from the refinement. (set occs to 0.00 so you still
see the coordinates in COOT)
Look at the difference map density and make a rough estimate of occupancy
from peak heights for a "fixed" bit of the conformers..
The relative ratios for different states s
