Hi everyone,
I've been looking at ways to convert an old hkl file from a CNS refinement (see
details below) into an mtz file.
F2mtz in ccp4 will do this once I have told it the fortran format of the hkl
file (below), and specified the data type and label for the input fields.
However, I'm not
Structure-function studies on protein-RNA complexes
A postdoctoral position is available immediately in the group of Dr. Graeme L.
Conn at Emory University School of Medicine in Atlanta GA, USA. Our lab uses
X-ray crystallography and complementary biochemical and biophysical methods to
address
Only Sharples i've had experience with was an old steam-driven model-
I wouldn't recommend that. Actually it looked a lot like the T1
at http://boto.ocean.washington.edu/file/show/2340
except for the motor.
An alternative you should consider is the sorval thermos (fisher?)
Heraeus Stratos Continu
Maybe it was a bit early to turn on TLS. Pseudomerohedral twinning of
a P21 crystal with a and c approximately equal often looks like C2221
with an appropriate transformation of the axes, that could explain the
high R-values.
George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
Unive
After having seen many Na+ ions very likely correctly built and refined and
many potential Na+ sites with
a very clear indication that the bond valence sum is already on the border
of being water and being an ion
I would say that Na+ binding in proteins happens quite often and probably
escapes "uno
But you are correct that refmac should allow the residuals to go negative.
This is what phenix.refine does when you do combined TLS + individual
isotropic ADP refinement.
Pavel.
On Tuesday 16 February 2010 10:54:49 Dale Tronrud wrote:
>I'm puzzled about this. If the B's listed by Refmac in the PDB
> file are the residuals that are to be added to the values derived
> from the TLS model, shouldn't they have a distribution with a mean
> value of zero? Why would one what
Dear all,
could anyone recommend a lab in Europe with a crystallization lab designed
with a good,
clever working environment for temperature/(humidity) control with
sufficient air conditioning backup, etc?
Especially if it includes lower and higher temperature environments (~10 or
30 deg).
I do not
Dear All,
Sorry for the not strictly crystallography-related question.
We are currently setting up a fermentation core and are considering
purchasing a T1 Sharples continuous flow centrifuge. It is a mid-range
capacity instrument. We will be processing bacteria and yeast.
I was wondering if anyon
I'm puzzled about this. If the B's listed by Refmac in the PDB
file are the residuals that are to be added to the values derived
from the TLS model, shouldn't they have a distribution with a mean
value of zero? Why would one what a minimal residual of 2A^2?
Aren't negative residuals not only p
dear fellow ccp4ers,
while trying to run a translation function in amore, with a certain
crystal form we get the above error.
in a little more detail, what we get is this ...
centred-overlap
stop >> traft << no reflection selected
AMORE: Fatal error in s/r TRAFT
the required input files ar
it looks like despite PDB now releasing coordinates with TOTAL B factors, the
Electron Density Server continues to add the TLS component on top of what
already is total B prior to map calculation.
(Just in case if someone else out there is wondering why solvent and ligands
[not included in TLS
Two possible points. Could there be a problem with twinning, or
spacegroup? The Rfactors seem rather high..
You dont say whether you have a non-crystallographic translation, but it
is faintly possible with 2 molecules that the SG is actually C222 ..
Or that twinning could be present - look a
Dear CCP Community,
We have processed protein scattering data in space group C2221 to a
resolution of 2.4 Å. The structure shows two protein molecules (chain A
and B) in the asymmetric unit, related by a local two-fold symmetry
axis. Initial rigid body refinement and subsequent full refinemen
A few years ago we thought that the bond valence method might provide
an answer to this problem and wrote a paper on the subject (Acta Cryst.
2003 D59 32-37). Subsequent experience has convinced me that although
this method works well for identifying ions such as Mg2+ and Ca2+ with
good resolution
Yes - we are puzzling over the same phenomena.
Look at this web site set up by Marjorie Harding
http://tanna.bch.ed.ac.uk/
It lists the likely coordination patterns.
We certainly have ideal Na bonding in our structure - but unfortunately
we wanted to find Ca which has a very similar pattern!!
Dear Jacob,
The latest WHAT IF/WHAT_CHECK (http://swift.cmbi.ru.nl/servers/html/index.html
--> Build/check/repai model --> template structure check) does ion checks in a
way similar to WASP. It does take symmetry into account and also checks if your
ions could be another ion. If you add a 'REM
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