Hello,
B-factors actually do have a physical meaning which is at least to some
extent reflected by the crystal structures as refined. This can be
demonstrated at higher resolution structures: when we created three
tiers of structures, better than 1.9 Å, 1.9-2.4 Å, and 2.4-3.0 Å,
structures in
what is this discussion about? please, try to be reasonable
Bohdan, structbio.org/bs
On 2019-02-01 10:05, vincent Chaptal wrote:
Hi Leo,
are you asking the question from the point of view of the user, or from
the beamline scientist allocating beamtime?
different answers then!
best
Vincent
On
Dear All,
pentagons of water are one of the old myths from the past millennium:
everyone talks about them, nobody has seen them. How many cases do you
have in your structure, how many have you analyzed in the PDB? In other
words, anecdotal evidence is fine, but what is their statistical
signi
Dear Dhiraj,
you may want to check our web service dnatco.datmos.org where you can
also generate 3D constraints for refinement in Phenix.
Best regards,
Bohdan, bs.structbio.org
On 2021-03-30 3:52, Srivastava, Dhiraj wrote:
Thank you everyone for the help. I am sorry about phenix related
que
Hello:
this may not be 100% relevant to the discussed issue but to add a data
analysis perspective: to be able to compare B factors in different
structures, they need to be scaled. We used primitive but in my opinion
functional linear scaling from 1 to 100 (Schneider et al. Acta Cryst D,
D70:
apologies for a brief note:
mmCIF is the default for structural biology data and the ways to avoid
its use are just improvisations leading to more improvisations.
Bohdan, bs.structbio.org
On 2023-05-19 11:48, Frank von Delft wrote:
Really, no CIF needed?
As far as I know, it's only in the C
Dear Colleague!
it is a pleasure to invite you to the upcoming conference of
ELIXIR 3D-BioInfo community, 3D-SIG of Intl. Soc. for Computational
Biology, and Czech ELIXIR
https://www.xray.cz/3D-bio-2023/
(apologies for multiple posting)
This structural bioinformatics event will be held in th
Dear Shawn,
hello to Rutgers!
dnatco.datmos.org reports local conformers in terms of *much extended*
A/B/Z concept. The conformers are called NtC classes and can be
generalized into a high-level structural alphabet CANA. NtC classes are
defined for dinucleotide blocks because to catch conform
