Chen,
First of all, it sounds funny that you can't integrate your data in C2 or P2.
That should be possible if your lattice is hP. But then if your Rmrg is OK in
P622, p622 is probably at least your (apparent) point group.
Second, I'm usually suspicious of SG P622. I would almost bet you're mi
Could it be that for some reason (like the components of your solutions) you
have Mg2+ in that site? Also, Magnesium
is a common "contaminant", trace amounts are usually present in one chemical or
another.
Subtle differences in the site might make it a "better" site for another
lighter ion (we
Hi Ivan,
these Dale Tronrud's slides might help you with understanding the maps:
http://www.ccp4.ac.uk/courses/stwk10/talk_files/Dale_The_Wonderful_World_of_Maps.pdf
Good luck!
Pavel.
On 6/29/10 6:35 PM, xaravich ivan wrote:
Dear CCP4BB,
I have come across something that might be pretty obv
Negative (or positive) density tells you what you that what you've
modelled is wrong.
If you have 1.15A X-ray data and it's telling you what you think is Ca2+
is not Ca2+, then I would think your X-ray data wins and your previous
structures lose (a lot can happen from one structure to the next
Woops! Sorry in case I just confused a lot of people. The number Felix
reports: n_xtals = 0.078 means that the structure solution should have
been "easy" (I.E. it could have been done with a crystal having only 8%
of the volume used), and indeed it sounds like it was a slam dunk. So,
it soun
On 6/29/2010 12:55 PM, Felix Frolow wrote:
BTW James Holton website calculate for this case 0.078 crystal
So far, every single one of these "reports" has come down to a
misinterpretation of the web interface. I am trying to make it clearer,
so I am interested in what values were entered
The part you are looking for is known as a "valve operator", at least in
the parlance of our supplier. Here's a cut & paste of the item we
purchased for pumping out our shipping dewars with a nominal 30mm O.D.:
V1000 Series Operator for 1" tube.
Part Numb
Quoting "Phil Evans" :
Can anyone explain what Zbyszek Otwinowski means by Chi squared?
If I understand properly, CHI**2 value as used in Scalepack is:
SUM(-Ij)**2/SUMsigma(I)**2 (I have to use formula editor to write
it properly, but the idea is clear) and is useful in exhibiting and
det
Looks atypical for 3-me-Lys, M3L, (usually in natively methylated products)
http://www.ruppweb.org/garland/gallery/Ch2/pages/Biomolecular_Crystallograph
y_Fig_2-27.htm
nor fits dimethyllysine, MYL, (via chem. red)
http://www.ruppweb.org/garland/gallery/Ch4/pages/Biomolecular_Crystallograph
y_Fig
Hi Christian
One guess would be one of the possible post translational
modifications seen for Lysine. acetylation or a triple methylation.
However propionylations and butyrylations have also been observed on
lysine.
It looks like you could build in waters, you may want to leave this
lysine
Can anyone explain what Zbyszek Otwinowski means by Chi squared? I can't find a
definition in any of his papers (though I may have missed it). Is there a
reference?
It doesn't seem obviously related to the chi squared distribution ("In
probability theory and statistics, the chi-square distribut
I second the hkl2map/SHELXCDE approach. Two complete examples
explaining how to do this for MAD and S-SAD cases are in my book.
I wish to emphasize the importance of
a) running enough trials
b) careful selection of resolution cutoffs
c) look at the solution distribution
d) play with SHELXE param
Dear All,
Can phenix.refine and Detwin in CCP4 handle twinning data with
multiple twinning law? Or there are
some other good programs can do this? If the data has some pseudo-meroheral
twin operators, can it be
treated as same as merohedral operates? Thanks very much!
Best
Yang
Applications are invited for a postdoctoral position to work on the
structure determination of membrane transport proteins critical in
cardiovascular function. The transporters we study have been linked to
human disorders such as cardiomyopathy, ischemia-reperfusion injury,
and various canc
On Tue, Jun 29, 2010 at 09:30:30AM -0700, James Holton wrote:
> Answering the question "should I even bother trying?" can be
> complicated, [...]
>
> -James Holton
> MAD Scientist
>
Since 'trying' may only take a semi-experienced user about 30min until they
could have a poly-Alanine trace of the
Answering the question "should I even bother trying?" can be
complicated, but I get asked that a lot at the beamline! I recently
incorporated a number of data quality formulas into a little interactive
web page here:
http://bl831.als.lbl.gov/xtalsize.html
which focuses on calculating how many
Alternatively you can force the fft to generate a map with the sfall
axiis order (sfall has a fixed axis order governed by the spacegroup)
From the fft documentation
You can set
AXIS
Eleanor
Kevin Cowtan wrote:
You could feed *both* maps through mapmask with AXIS X Y Z to convert
them to t
I would say CC-anom > 0.3 or even 0.2 (note that the scala CC-anom is defined
on I not F)
Phil
On 29 Jun 2010, at 14:37, Frank von Delft wrote:
> I've found the scala CC-anom significantly underestimates the anomalous
> signal, relative to e.g. xprep. I don't know why that is, but the latter
I've found the scala CC-anom significantly underestimates the anomalous
signal, relative to e.g. xprep. I don't know why that is, but the
latter seems to agree with what shelxd is happy with.
Cheers
phx
On 29/06/2010 10:35, Graeme Winter wrote:
Hi Murugan,
One useful indicator of raw ano
Dear All,
Don't miss out on the P-CUBE meeting in Grenoble in September! Sign up today
underwww.p-cube.eu. The registration deadline is June 30. 2010.
See you in Grenoble
P-CUBE Management Team
***
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Department of Biochemistr
Dear Murugan,
Am 29.06.10 11:05, schrieb Vandu Murugan:
Dear all,
I have collected a 2.7 angstrom home source data with Cu-Kalpha
source for a protein with 6 cysteines, with a multiplicity of around
23. I need to know, is there any significant anamolous signal present
in the data set, si
Hi Murugan,
One useful indicator of raw anomalous signal is the ANOMPLOT graph
from Scala - this shows the differences between reflections compared
with the expected differences. If the gradient of the plot is 1
there's no more differences that you would expect. If the gradient is
more than one th
Dear Murugan,
you can use the program hkl2map from Thomas Schneider, available at
http://webapps.embl-hamburg.de/hkl2map/
It's a graphical interface to the programs shelx c/d/e which are available from
http://shelx.uni-ac.gwdg.de/SHELX/index.html
With SAD data you want to look at the d"/sigma li
Vandu Murugan wrote:
Dear all,
I have collected a 2.7 angstrom home source data with Cu-Kalpha
source for a protein with 6 cysteines, with a multiplicity of around
23. I need to know, is there any significant anamolous signal present
in the data set, since there is no good model for my pro
Dear all,
I have collected a 2.7 angstrom home source data with Cu-Kalpha source
for a protein with 6 cysteines, with a multiplicity of around 23. I need to
know, is there any significant anamolous signal present in the data set,
since there is no good model for my protein. Can any one tell, w
You could feed *both* maps through mapmask with AXIS X Y Z to convert
them to the same axis order.
You may also have a problem with the maps having different XYZLIM
ranges. In that case, using XYZLIM MATCH on the second run of mapmask to
match the second map to the first should fix it.
Kevin
Can you attach the first 50 lines of your hkl file?
Eleanor
Yogesh Gupta wrote:
Dear Experts,
After a new installation on Mac OS 10.6, i am getting this error (related to
f2mtz) during the "Find SITES" step by SHELX in Autosharp.
Data line--- LABO H K L FA SIGFA ALPHA
Number of columns to be
Dear all,
A tribute to Lodovico (pictures + letters + a song) can be found on
http://www.crystalerice.org/Erice2010/Lodovico/index.htm
Fred.
Dear Frank,
DIRAX is very good at finding the twin lattices in case of non-merohedral
twinning. In the reticular case you might want to use the LEPAGE-TWIN routine
in PLATON to find the correct subcell.
My collegue, Martin Lutz, suggests to change the measurement temperature in
order to chang
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