On 16/12/2010 12:24, Ian Tickle wrote:
I think this is how the Oxford CRYSTALS software (
http://www.xtl.ox.ac.uk/crystals.html ), which has been around for at
least 30 years, deals with this issue, so I can't accept that it can't
be made to work, even if I haven't got all the precise details
str
Ian Tickle replied:
(freezing & soaking can easily induce > 1% and sometimes > 5% change),
is surely the reason that Fo-Fo maps never caught on!
I've been curious about this unit cell constant mis-matching for a
while. If I understood well, Perutz tried to exploit the effect
There seems to be a clue in the text?
"Models were displayed and figures were produced with PyMOL (Delano,
2002)", which you can read at the end of section 2 "Materials and Methods".
ANDY DODDS wrote:
Hello,
I was wondering what people used to generate difference map images of,
say, a ligan
Link,Todd M wrote:
... I did not find an equal web support page for Windows.
It just isn't needed. If there is a windows version of a program you get
to "download, install, run" and then get on with your life.
Jon
Sanishvili, Ruslan wrote:
.. Reasons for discriminating
5-10 micron beams (minibeam) from ca 1 micron (microbeam) might have
been not so much their size but what it involved to achieve these sizes.
Might I ask - do you really get data from 1 micron protein crystals? The
reduction in
James Stroud wrote:
... What is the
operation to reindex such that real space is rotated 180 about z? These
are in P212121.
Isn't that the 21 along z in your orthorhomic space group? Just apply it
to your MR solution instead, and add an affine normaliser if needed to
superpose the solutions
Dear Owen,
The GSAS package can do that:
http://www.ccp14.ac.uk/solution/gsas/
It is important to put some values for the solvent contribution if you
want to get a meaningful pattern. Shout if you need a hand.
Good luck,
Jon
wob wrote:
Hi,
I'm looking for a free program for calculating p
Borhani, David wrote:
...
but I think pretty much everyone has converged on using it for the
past many years.
Many small molecule crystallographers seem to refine on intensity and so
avoid need this procedure. Towards the end of the recent thread "Wilson
plot from truncated.mtz" it had seeme
You may be able to check whether the cyrstals are protein or detergent
this using powder diffraction. (please excuse the shameless plug):
Acta Cryst. (2008). A64, 169-180 "Powder crystallography on macromolecules"
I. Margiolaki and J. P. Wright
http://journals.iucr.org/a/issues/2008/01/00/sc5011
Dear Ed,
I don't see how you "decouple" symmetry mates in the case of a wrong
space group. Symmetry mates should agree with each other typically
within "R_sym" or "R_merge" percent, eg; about 2-5% . Observed and
calculated reflections agree within "R_Factor" of each other, so about
20-30%. Th
It'd be interesting to determine the validity of the assumption that
absorption is simply a function of frame number.
... and direction. See, eg:
Acta Cryst. (1995). A51, 33-38[ doi:10.1107/S0108767394005726 ]
An empirical correction for absorption anisotropy
R. H. Blessing
Best,
Jon
Think this bounced last time I tried to mail it in, a simulator exists at:
http://fable.sourceforge.net/index.php/Farfield_Simulation
Jon
Eleanor Dodson wrote:
ZO has a good point - it is a pain trying to get decent simulated
material - maybe there is an employment opportunity here?
Eleanor
> ...One thing I don't like about it is that
columns can be randomized (i.e. X, Y, and Z can be in any column)
Rows too! Some anarchists even re-order the symmetry operations ;-)
-Jon
James,
At least for diffraction experiments; the photon scatters off of the
*crystal lattice*, not any individual electron, so you can conserve the
momentum of the photons and the macroscopic crystal without the crystal
recoiling too much.
Best,
Jon
Murray, James W wrote:
Dear All,
Wh
Fit2d is perhaps the 'gold standard' for making powder diagrams:
http://www.esrf.eu/computing/scientific/FIT2D/
See also:
http://www.datasqueezesoftware.com/
For source code try:
http://cctbx.sourceforge.net/current_cvs/python/iotbx.detectors.html
Good luck,
Jon
-Original Message
"Workshop on the Development and Direction of Powder Diffraction on
Proteins"
ESRF, Grenoble, France, 22-23 June 2007
http://www.esrf.fr/events/conferences/PowderDiffraction
The investigation of protein structures by high-resolution powder X-ray
diffraction has been established as a complement
Do you have any data to support the implication that Acta F will have
a lower citation factor than Acta D?
Checked a web of sciences "Citation report" for a search with the year
2005 and "source titles":
ACTA CRYSTALLOGRAPHICA SECTION F STRUCTURAL BIOLOGY "AND"
CRYSTALLIZATION COMMUNICATI
Kevin Cowtan wrote:
Acta D has for some reason a rather poor impact rating, and J. Appl.
Cryst. a rather better one.
There is no outlier rejection in the calculations for journal citation
reports (eg: impact factors).
Congratulations to: Spek AL, "Single-crystal structure validation with
t
> The mathcad image processing module is too expensive for my taste.
My university has a campus- wide license for Matlab, so it's *free* for me...
I have no idea of what it would cost to purchase.
[reminder: never compare "educational licensing" with giving drugs to
schoolchildren.]
For so
Randy J. Read wrote:
On Jan 22 2007, Eaton Lattman wrote:
Will someone knowledgeable tell me what the present state of full 6
dimensional searches in molecular replacement?
...
If the latter, our feeling is that it isn't worth it. We've tried the
full search option on a couple of monoclini
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