Hi,
Probably a stupid question.
Could you multiply a, b and c cell dimensions by 2 or 3 (to give 8 or 27
structures) and restrain well defined parts of structure to be ‘identical’ ? To
give you a more NMR like chemically sensible ensemble of structures?
Ben
> On 18 Mar 2023, at 12:04, Helen Gi
Hi,
I have had twinning with P61, which makes it look like P6122. This is with
slightly asymmetric dimer.
You could try mol replacement in P65, and refine with twinning on. Maps should
look better if correct. Ben
Sent from my iPhone
> On 9 Jun 2021, at 10:13, Randy John Read wrote:
>
> I
his is no longer true, I’m happy to learn of it.
Charlie
> On Apr 28, 2020, at 6:40 AM, benjamin bax <mailto:ben.d.v@gmail.com>> wrote:
>
>
> HI Fred,
>
> I still use command line version of lsqkab to do this kind of DNA fitting -
> script below only uses maincha
HI Fred,
I still use command line version of lsqkab to do this kind of DNA fitting -
script below only uses mainchain atoms (not bases) which helps if you have
different DNAs.
Chain E and F are DNA.
Ben
./lsq-hinge-6fqv-bin-EV-B.com > lsq-hinge-6fqv-bin-EV-B.log
cat lsq-hinge-6fqv-b
In PDB files you could put all information about protein delivery buffer,
crystallisation conditions and cryo conditions in
REMARK 280
(and pull it through in refmac with keyword
pdbout copy remarks 280
)
Where are you meant to put all the information about what could be in your
crystal in mmc
Hi Katherine,
One possibility could be that you have occupancy of 0.5 and that ligand
binding at one site in the crystal distorts a second site so it cannot bind
ligand.
Occupancy refinement is not always very stable.
If you are looking at two structures on top of one another - refinement
Hi Harry,
I think some old stuff from Birkbeck crystallography teaching labs. went to
science museum.
However, picture of
Enraf-Nonius Weissenberg X-ray camera, model Y809, (X-ray diffraction camera) -
from 1968 - does not look quite like what I remember.
https://collection.sciencemuseum.or
We are advertising for a Senior Laboratory Technician Protein Purification in
the Medicines Discovery Institute at Cardiff University, UK.
The goal of the newly-established Medicines Discovery Institute in Cardiff is
to translate world-leading research on scientific understanding of disease
Hi,
Looks like you have some density for same conformation as in A chain.
It could be you have two (or more) conformations for some parts of the
structure in MolB. It is often tricky to sort out when you have two
conformations for residues and map is ambiguous (and at 2.8A).
I would rigid b
Hi Trevor,
Some of my colleagues came across a misinterpreted structure published in
Acta D., a couple of years ago.
They raised the issue with the editors of Acta D., who were most helpful in
getting the issue sorted out.
My impression is that the journals are the responsible for the papers
Hi Khoa,
How many rounds of refine and rebuild have you gone through on the graphics?
Have you tried Lorestr in CCP4 (Automated refinement of macromolecular
structures at low resolution using prior information, Oleg Kovalevskiy, Robert
A. Nicholls and Garib N. Murshudov).
Ben
[At 2.9A res
How about
WONKA and OOMMPPAA: analysis of protein–ligand interaction data to direct
structure-based drug design?
Ben
On 7 Jun 2017, at 07:59, Eleanor Dodson wrote:
Many years ago I wrote code to label waters with a code related to the
residue/atom they were Hbonded to , so then you could
'Most distances between bonded atoms weresettled longago
to highaccuracy, but,in the caseof
hydrogens, the values in common use often differ by
as muchas 20%.'
Phenix / MolProbity
Hi,
A think a detailed discussion is off topic for CCP4 bb.
https://www.quantiki.org/wiki/quantum-sock-theory
Ben
On 2 Apr 2017, at 00:31, Phoebe A. Rice wrote:
At long last, a brilliant theoretical framework for observations previously
dismissed as mere discrepancies!
This being Saturday
Hi Alun,
1. What does phenix.xtriage think of the dataset?
2. What kind of redundancy do you have in the dataset?
3. Sometimes with a large crystal and a small beam the twin fraction varies as
you rotate the crystal and illuminate different parts of the crystal (which can
have different twin fra
You could try the diffraction anisotropy server:
http://services.mbi.ucla.edu/anisoscale/.
Sometimes it helps maps become more interpretable.
Ben
On 26 Jan 2017, at 14:11, Pooja Kesari wrote:
We have a 2.6 A structure showing four chains in an asymmetric unit. Our
protein is 360 res
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