Hi,
I’ve just double-checked with the organisers. We’ve been asked to agree to
having our talks recorded. Some speakers might opt out, but the ones that are
recorded will be available for participants to view at a more convenient time.
Randy
> On 26 Aug 2021, at 22:22, Joel Tyndall wrote:
>
Dear Eleanor,
I indeed used r/tefmac for the refinement and it came up with the values
HKL (a=0.56), KH-L (a=0.44). It would be interesting to see if a
refinement in P3221 would come up with the same occupancies for the
alternative conformations for the "extra" chain on the 2-fold axis. It
Hi everyone,
I am working on refinement of a protein-NA complex. It has a dna-rna
duplex. How do we build a dna rna duplex in coot. I was able to optimize
the RNA chain using Rcrane, is there a similar tool to work on DNA chain?
Could anyone please suggest a better way for the refinement of
Dear Peer and Eleanor,
This is indeed what I am suspecting: If the "twinning operator" in P32 puts 4
out of 5 protein chains on top of symmetry mates, is the "true" space group
then P32, with 5 twinned chains, or P3221 with 4 normal chains and 1 chain on a
special position? I would vote for
9 am CEST (Norway). Pretty early for our North American colleagues, especially
those on the west coast!
> On 27 Aug 2021, at 05:18, Robert Rose wrote:
>
> Does the workshop start on August 31 at 9 am GMT?
>
> On Thu, Aug 26, 2021 at 2:27 PM Randy John Read wrote:
> Hi,
>
> I’ve just learned
Dear Lijun,
with this argument I agree: the interactions between the two orientations of
the “twinned” chain and the neighboring molecules will be different and the
interacting side chains will almost certainly have different orientations,
which necessitates a twinning of the whole structure.
Hi Kay,
Can you also comment on Rfree set selection? It seems thin shell might be
preferred in these cases?
jbb
Jeffrey B. Bonanno, Ph.D.
Department of Biochemistry
Albert Einstein College of Medicine
1300 Morris Park Avenue
Bronx, NY 10461
off. 718-430-2452 fax. 718-430-8565
email
How P3221 can be an option if it assumes chain on axis? I guess I'm missing
something, but per my belief only those sg will be possible for which there is
no axis going through the extra molecule. P1 sg looks the only correct option
here in my humble opinion.
Democracy (voting) depends on
I believe it is a twin from P32.
Not like the assignment of double conformations with partial occupancies to
small part of asu, for examples, a side chain of lysin or a small fragment of a
protein, which have both conformations stayed in the same specific asu at the
same time. For this p3221
Dear Herman,
there is no freedom to choose between twinned-P32 (5 chains) and
untwinned-P3221 (2 chains plus 0.5 chain in two orientations) or even vote; it
is either one or the other, and there should be a difference in R values.
Why? A twin operator leads to addition of intensities whereas a
P1 is always a "correct" answer but this data says there is a three fold
axis.
Twinning generates an apparent 2 fold in the diffraction pattern, and with
four of the five molecules obeying that 2fold, and twin factors 0.56/0.44
that will appear pretty exact..
And the NC transl;ation disguises
Dear Vaheh,
I agree with you, at least in your last statement. I guess we all agree that
certain molecules can occupy special positions on true rotation axis. Strictly,
this is only possible if the molecule obeys the rotation symmetry. For water
molecules on 2-folds you already have to make
Dear Herman,
The answer probably depends on the impact of the "extra" chain on the
sublattice. If there is no impact the "true" space group is P3221 with
one chain on the special position. If the swapping of the extra chain
influences the sublattice P32 (or C2 or P1, as pointed out by Kay)
Dear Lijun and others,
As Kay rightly pointed out, twinning is fundamentally different from e.g.
disorder or alternative conformations. However, it does not depend on a chain
or side chain rapidly jumping between two states, but whether they are within
coherent length of each other. Since most
I just change MODEL 0 to MODEL 1 then it works fine.
John
On Fri, Aug 27, 2021 at 11:03 AM Schreuder, Herman /DE <
herman.schreu...@sanofi.com> wrote:
> Dear Nick,
>
>
>
> I had just looked at a pdb downloaded from the alphafold server without
> problems. However, then I realized that I had
Dear Herman:
if you say “twinned” chains, then it already means same thing of the two and
the side chain interactions could not be different (as you can see only one
copy in the output coordinates), unless you talking about borders between twin
pieces.
In this situation, the only I could
Has anyone made use of an Alpha Fold PDB as opposed to CIF. On the half
dozen or so I have tried to read into CCP4mg or coot the PDB has always
failed but the CIF is fine. I can then write out a PDB if I want.
I could add to the conspiracy theories that this is EBI trying to
normalise use
Dear Jeffrey,
just using thin shells of reflections for the test set might not be
enough to eliminate any correlation to working set reflections. The
distance of the test set reflections in reciprocal space, after applying
the NCS rotations in reciprocal space, to any reflections of the
Just get rid of the PDB header minus CRYST1 IIRC and it'll work. Some weird
formatting problem.
On Fri, 27 Aug 2021 at 15:50, Nicholas Keep
wrote:
> Has anyone made use of an Alpha Fold PDB as opposed to CIF. On the half
> dozen or so I have tried to read into CCP4mg or coot the PDB has always
Dear Nick,
I had just looked at a pdb downloaded from the alphafold server without
problems. However, then I realized that I had looked at the alphafold model
after I had it superimposed on my own structure. Loading the alphafoldmodel
directly in coot failed for me as well.
By looking into
Hi
I mentioned this issue to Stuart McNicholas a couple of weeks ago but I'm
assuming he's on his Summer hols as I haven't had a reply yet.
In QTMG I get a pop-up telling me there's a problem with a DBREF line in the
PDB file.
Harry
--
Dr Harry Powell
> On 27 Aug 2021, at 16:03, Schreuder,
upper limit for the molecular weight of this molecule?
David Cobessi solved a structure with heme on a crystallographic 2-fold.
https://www.ncbi.nlm.nih.gov/pubmed/11752777
Heme is almost, but not quite, 2-fold symmetric.
eab
Peer Mittl wrote on 8/27/2021 9:55 AM:
Dear Vaheh,
I agree with
Hi Jeffrey,
good question. Both twinning and NCS may couple reflections across free and
working sets, and this should be avoided by proper selection - otherwise Rfree
is biased towards Rwork. Selecting thin shells should be a good option, and can
be done in SFTOOLS (or DATAMAN, or SHELXPRO).
Hi Dirk and Kay,
Excellent, many thanks for the refresher!
jbb
Jeffrey B. Bonanno, Ph.D.
Department of Biochemistry
Albert Einstein College of Medicine
1300 Morris Park Avenue
Bronx, NY 10461
off. 718-430-2452 fax. 718-430-8565
email jeffrey.bona...@einsteinmed.org
-Original Message-
The Furukawa lab at Cold Spring Harbor Laboratory (CSHL) has a postdoctoral
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biology and biochemistry. We work on ion channels and membrane protein
complexes involved in the neurobiology of learning/memory,
Postdoctoral Research Associate
University of Liverpool - Department of Cardiovascular and Metabolic Medicine
Location: Liverpool
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