Dear All, sorry for this off-topic inquiry. I am interested in knowing about
the current scientific research in Singapore but have had hard time finding
the most up-to-date articles/comments on this. All I could find are the
articles a few years back in Science and Nature.
Would appreciate a point
Dear Andy,
We have seen this error since forever on our Ubuntu boxes (I believe starting
from ubuntu ver. 8.04). This is what the latest version of imosflm outputs on
startup:
lbbspc2 ~ > imosflm
MOSFLM_EXEC set to /usr/local/lbbs/ccp4/current/bin/ipmosflm
[: 180: =: unexpected operator
testing
Hi Todd,
in addition to all other suggestions, here is some basic sanity check that
you can do in no time:
- how the R-factor vs Resolution plot looks like?
- did the bulk-solvent correction was done right (what are k_sol and B_sol
values)?
- plot the scatterer graph Fobs vs Fmodel and see if t
Hi Chandan,
The answer to your question about buffers is to use any buffer that does not
bind to metal ions like zinc for example. I have used TRIS and MES myself
successfully for crystallization of zinc finger proteins. What kind of zinc
fingers do you have? If there is histidine then you can
Hi Dirk,
This example compares integration software in combination with the
scaling program, which is what usually happens. Obviously, the scaling
program does more than just scaling, it also handles rejections. It is
possibly this procedure that makes most of the difference. For
example, the defa
Are you sure that the space group is right? P4132 is cubic, so the
spots should have equal spacing on the detector, i.e., squares. Don't
you have rectangles? Even the least distorted spots towards the
beamstop (bottom right?) seem to be non-square rectangles.
JPK
On Fri, Jan 28, 2011 at 3:07 PM,
Hi,
This sort of problem can occur if you are missing your lowest resolution
data and/or your model for the bulk solvent is inappropriate. You might
want to double check these issues.
With 80% solvent you have to be careful when choosing your contour level.
If you are a fan of normalized m
Hello Hui,
This is also done quite easily in coot. Go to Extensions --> maps -->
Transform map by LSQ model fit...
Eric
Eric T. Larson, PhD
Biomolecular Structure Center
Department of Biochemistry
Box 357742
University of Washington
Seattle, WA 98195
email: l
Herman
Thanks. 5-10 degrees is certainly high whatever definition one uses.
In the list I gave, I didn't include "relative to the angular separation of the
diffraction spots in reciprocal space."
I would like to say that I didn't include it to see if anyone else came up with
this one.
It does work well. That is great!
Many Thanks!
On 1/28/11, Pavel Afonine wrote:
> Hi Hui,
> (sorry for non-ccp4 recipe)
> IF I understand correctly what you want to do, then I guess you can achieve
> this using Map Superposition:
>
> http://www.phenix-online.org/documentation/superpose_maps.htm
Hi Andy
I haven't seen that one before. I have a Maverick Meerkat at work, so
I can check on Monday to see if it's something that is peculiar to
that. On my old Jaunty Jackalope at home, I don't see the error when I
install the 32-bit Linux version.
Can you let me know if iMosflm works in
To the CCP4bb,
I am working on installing the latest version of iMosflm (version
1.0.5) on my computer (running Ubuntu 10.10 (Meerkat). I've followed the
installation instructions at the following link. I also have CCP4 ver. 6.1 and
ActiveTcl ver. 8.4.19.3 installed and working (as fa
Hi Hui,
(sorry for non-ccp4 recipe)
IF I understand correctly what you want to do, then I guess you can achieve
this using Map Superposition:
http://www.phenix-online.org/documentation/superpose_maps.htm
and/or Structure Comparison tools in PHENIX:
http://www.phenix-online.org/documentation/stru
Dear All,
I have the problem as follows, but I can not find the corresponding
solution. Can somebody give me some suggestions?
Many Thanks,
Hui Rong
*
[PyMOL] aligning electron density maps
Eksterowicz, John
Not sure if you ever got an answer to the original question (but I have had
some mail mishabs today, so perhaps some messages are missing in my thread)
Anyway: for sure NO - you cannot process the data with different parameter
settings and then merge the different integrations as a way to gain in
I see two questions here:
-Can we assume an unrealistically low mosaicity in order to reduce
overlaps.
-Is there any benefit in merging data from the same frames integrated with
different strategy?
As for cheating on the mosaicity, which I euphemistically call "peak sampling",
I think it can gi
A few things that might be worth looking at:
1. How is your beam divergence varying as you fix mosaicity at different
levels? Does it look relatively stable at a realistic value for the
beamline? If I'm remembering correctly, mosaicity and beam divergence
are highly correlated within mosflm.
Jim's comment brings us back to the Dauter in us, or better the Dauter which
should be in us.
Data Data Data !
Before shooting take a moment and think about the experiment.
How do you collect the best possible data from a bad crystal. Investing time at
the beginning always pays off (unless the be
You should know that your crystal mosaicity is a physical property of your
crystals and the diffraction experiment. Generally, it is anisotropic
though most programs output a single value. How can that single value
describe what is really happening in your experimental data?
You can do anything
On Fri, Jan 28, 2011 at 9:35 AM, wrote:
> [...] due to the 3-dimensional profile fitting.
what is the specific difference between 3-d profile fitting and using
a sliding window of more than one image?
-Bryan
A version of the Daresbury Laue programs that can process ADSC CCD data (Q-210,
Q-315, etc.), and also has some improvements to the indexing routine for the
case of sparse diffraction patterns, is available from CHESS,
ftp://waterline.chess.cornell.edu/pub
Some documentation (as text files) an
For me, it means a reflecting-range (as defined by XDS) of 5-10 or more degrees
and spots being visible on at least 5 or more frames (when using 1° frames).
Good crystals (in our hands) have reflection-ranges in the order of 0.5-1.0°.
Of course we trust that the synchrotron where we measure (ESR
Can people say how "high mosaicity" is defined. High relative to what?
Is it high relative to the rotation range for each image, high relative to the
incident beam divergence, high relative to the (angular) detector resolution or
something else?
Regards
Colin
From: CCP4 bulletin boar
Dear all,
There is a staff member vacancy for a Research Software Developer at
the EMBL Unit in Hamburg, Germany. The post holder will have a leading
role in technical implementation and scientific development of the
ARP/wARP software for crystallographic structure determination and the
b
My experience (unpublished) is that XDS works very well for high-mosaicity
crystals due to the 3-dimensional profile fitting. For low mosaicity crystals,
I did not notice much of a difference between different programs. However,
since bad crystals tend to have a high to very high mosaicity, I fu
On Jan 28, 2011, at 8:45, "Bosch, Juergen" wrote:
> Mark Robien and I did a "systematic" study on about 30 data sets while we
> were at SGPP.
can you name the detector(s)?
-Bryan
James Swindell, UGeorgia had a presentation "Evaluating the role of data
reduction approach on the success rate on Sulfur-SAS phasing for a moderately
diffracting crystal" at PittCon, Oct 2009, comparing HKL, d*TREK, XDS, Proteum2
& Mosflm
MfG, rgds,
Eric
Phone: +49 (721) 50997-5311 /
... but, back to the main point, my advice would be to only limit the
mosaicity, to get better completeness by avoiding overlaps.
Its not ideal, in the sense that you would be over-estimating the
partial fraction of most partial reflections, and thus systematically
underestimating intensities
Interesting! But when will it be published? :-)
On 1/28/11 8:45 AM, "Bosch, Juergen" wrote:
Yes.
But we have not published this.
Mark Robien and I did a "systematic" study on about 30 data sets while we were
at SGPP. The easy cases can be processed with anything the difficult cases
worked
Hi Bert,
here is one anecdotal evidence: a couple of years ago, I had one real
in-house 3 A data set from a crystal after a quick iodide soak and
processed the images with denzo/scalepack, mosflm/scala and xds/xscale.
I got lower Rsym, higher I/sig(I) and better anomalous signal with xds.
Mor
Yes.
But we have not published this.
Mark Robien and I did a "systematic" study on about 30 data sets while we were
at SGPP. The easy cases can be processed with anything the difficult cases
worked only with XDS.
This was mostly SeMet data or HA data, so de novo phasing no MR stuff.
If you compar
I have heard this before. I'm wondering though, does anybody know of a
systematic study where different data processing programs are compared with
real-life, non-lysozyme data?
Bert
On 1/28/11 7:58 AM, "Bosch, Juergen" wrote:
I was a bit reductive with my statement (iPhone)
The equation
I was a bit reductive with my statement (iPhone)
The equation below is suppose to read:
If you have bad data, then you need to process with XDS in order to get the
maximum out of your data.
Thanks Tim,
Jürgen
-
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Bioch
Dear Jürgen,
is this an assignment operator or an equal sign? For if it's the latter it could
read that the result of processing data with XDS are bad data, which is rather
rude and probably not what you meant.
Tim
On Fri, Jan 28, 2011 at 06:55:43AM -0500, Jürgen Bosch wrote:
> Bad data = proces
Ah, yes, I was missing that. The statistics will be wrong. But in principle I
will get an mtz with better data, because I am integrating more observations
which would have been rejected by being missed at low resolution if the
mosaicity was set too low or being rejected by overlaps at high resol
Jose - you're missing the fact that the same dataset processed in
different ways are not statistically independent datasets! Increasing
the multiplicity for independent data reduces the uncertainty because
the calculation of the SU assumes statistical independence.
Cheers
-- Ian
On Fri, Jan 28,
Bad data = processing with XDS
Jürgen
..
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Phone: +1-410-614-4742
Lab: +1-
Hello all,
I have been trying to squeeze the most out of a bad data set (P1, anisotropic,
crystals not reproducible). I had very incomplete data due to high mosaicity
and lots of overlaps. The completeness was about 80% overall to ~3A. Yesterday
I noticed that I could process the data much bette
Dear Hao Quan,
Yes I forgot about CHESS; apologies.
Charles Ballard helped with the recent installation at the Diamond
Test Beamline.
The modifications to read the Photonic Science detector Laue images on
the Diamond Test Beamline
have been made by Karen Ashton and Steve Kinder based at the Daresbu
Hi all,
Just a reminder, as deadline is approacing
DEADLINE TO APPLY FEBRUARY 28th
COURSE ANNOUCEMENT
EMBO 2011 Practical Course - Exploiting Anomalous Scattering in
Macromolecular Structure Determination
ESRF-EMBL, Grenoble, France, 6 - 10 June 2011
The EMBO 2011 Practical Course on Exploit
Dear Rex,
the most popular one seems the Daresbury Laboratory Laue Software Suite,
available via http://www.srs.ac.uk/px/jwc_laue/laue_top.html
I have not, though, managed to compile the whole suite.
There is also a commercial product from renzresearch.com, as M. Blakeley has
pointed out to me.
Dear Rex,
I can speak for the 'Daresbury Laue Software Suite', which is available with
full documentation and tutorials from :-
http://www.srs.ac.uk/px/jwc_laue/laue_top.html
A wide range of validation tests involving both biological and chemical
crystallography have been made of the software and t
What programs are available for processing Laue data to produce an intensity
data set?
Are explanatory notes or publications available?
Rex Palmer
Birkbeck College
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