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
Hi all,
I have determined the structure of a protein at 3Å resolution. The protein
has 6 chains in the asymmetric unit. In all these 6 chains I see a density
near tyrosine which is at a distance of 2.1 from the OH group of tyrosine.
Since this distance is short for a hydrogen bond we are skeptical
Dear Lumbini,
Thank you for sharing this picture.
Considering the low resolution and modest quality of your map, as
manifested in the "blobbiness" of the side chains near the green peak, the
"short distance" you mention is perhaps quite imprecise and thus not such a
barrier to tentative
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
Dear CCP4 Community,
My lab at Stanford (https://rogala.stanford.edu) is thrilled to announce a
newly funded position for a postdoctoral scholar with a background in
structural biology or protein biochemistry. Expertise in working with
either integral or peripheral membrane proteins will be an adv
