I googled on the subject and found that a discipline that deals with this type
of problems (measurements) is called the Decision theory. It uses statistics to
estimate probability of certain events (results of measurements). So,
everything depends on a decision that someone needs to make. A sin
8. Empty the carboy and fill the supply lines and wash stations with
20% ethanol at the end of the day. (Requires decontamination in this case)
Best regards,
Dmitry
On 2013-03-13, at 10:04 PM, Viswanathan Chandrasekaran
wrote:
> Dear All:
> Thank you for your responses. Here is a su
Dear Lucas,
Thank you for your help!
Wei
At 2013-03-13 23:05:54,Lucas wrote:
>That probably won't be very precise. A better option would be doing an
>advanced search, then select Structure Features -> Number of Entities
>as a protein query, select "protein" as entity type, and then a very
>
Dear All:
Thank you for your responses. Here is a summary of suggested fixes:
1. Cleaning the supply carboy and lines with bleach and flushing
thoroughly with DD water afterwards
2. Adding 0.02% sodium azide to the protein
3. Adding 0.02% azide to commercial screens
4.
Slightly off the topic, but still potentially relevant in terms of realistic
experimental error: when dealing with the small volumes typically used in
crystallization (say 1 uL + 1 uL drops), and using a 10 uL pipette, the errors
are fairly high (more like 30% than 5-10%), leading to a lot of
n
I think that in statistics you can build a model that describes (and predicts)
the uncertainty. So if you have done similar (!) replicate experiments, from
which you can build the model, you can apply it to a single observation and
provide a reasonably good guess for the value that you were meas
On Mar 13, 2013, at 1:36 PM, Ed Pozharski wrote:
But what if I only have one measurement worth of sample?
Is it proper to use statistical analysis for a single measurement? I thought
statistics, by definition, means multiple measurements.
Alex
Ian,
On Wed, 2013-03-13 at 19:46 +, Ian Tickle wrote:
> So I don't see there's a question of wilfully choosing to ignore. or
> not sampling certain factors: if the experiment is properly calibrated
> to get the SD estimate you can't ignore it.
>
So perhaps I can explain better by using the s
The work at Hamburg was on insect flight muscle. It is usually quoted as the
first x-ray diffraction using a synchrotron. The work is acknowledged as
pioneering in John Helliwell's book.
Of course the first data collection on a synchrotron was much earlier. A good
account can be found here
htt
I never would have survived the dress code back then.
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Anastassis
Perrakis [a.perra...@nki.nl]
Sent: Wednesday, March 13, 2013 2:27 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] first use
Use HKL2000
Dr Felix Frolow
Professor of Structural Biology and Biotechnology, Department of Molecular
Microbiology and Biotechnology
Tel Aviv University 69978, Israel
Acta Crystallographica F, co-editor
e-mail: mbfro...@post.tau.ac.il
Tel: ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 054
Dear colleagues,
We have some diffraction data from small peptide crystals, the shape of
diffraction spots looks normal, and resolution is beyond 2A. The data were
collected with 5 degree rotation per image. Later on we found it is hard to
do index. Does anybody know some skills to figure this pro
> OK. Other words, what is potentially removable error is always
> statistical error, whether it is sampled or not.
Clarification - what I meant is potentially removable by proper sampling
and reducing standard error to zero with infinite number of
measurements. Not removable by better calibrati
The precision must be obtained either from multiple measurements which must
be representative of the measurements you propose to make, or if the
measurement consists of a count (say of photons) then from counting
statistics, or a combination of the two. This must be done by either by
prior calibra
Nice account on the subject
J Synchrotron Radiat. 2010 July 1; 17(Pt 4): 433–444.
Published online 2010 May 14. doi: 10.1107/S0909049510011611
Impact of synchrotron radiation on macromolecular crystallography: a personal
view
Zbigniew Dauter,a,* Mariusz Jaskolski,b,* and Alexander Wlodawer,c,*
Ian,
thanks - I think I had it backwards after reading your first post and
thought of controllable errors being those that can be brought "under
conrtol" by sampling, whereas uncontrollable would be those that cannot
be sampled and therefore their amplitude is unknown.
Yet you also seem to agree
And indeed this experiment was done properly ... in a suit and tie!
http://www.embl-hamburg.de/aboutus/general_information/HH_about/history/HH-holmes.jpg
A.
PS The journal is indeed a bit obscure ...
On 13 Mar 2013, at 20:22, DUMAS Philippe (UDS) wrote:
> Jean Witz (now deceased) once told
Jean Witz (now deceased) once told me that the following paper is the first
one mentionning data "collection" on a synchrotron.
The journal is not really "obscure" and the paper should easily be found.
The work was done in Germany, if I remember well.
G. Rosenbaum, K.C. Holmes and J. Witz, Synch
Kay,
> the latter is _not_ a systematic error; rather, you are sampling (once!) a
> statistical error component.
OK. Other words, what is potentially removable error is always
statistical error, whether it is sampled or not.
So is it fair to say that if there are some factors that I either d
Sivaraj Ramesechan was outlining the physics of multiple wavelength anom
scattering in the 1960s as a method for solving insulin.
It was purely theoretical then; no instruments to make the measurements..
Eleanor
On 13 Mar 2013, at 17:19, Peter Moody wrote:
> When I started my PhD (in 1980!) at
Dear Ian, Herman, and others
What an active and responsive bulletin board!! Thanks for the helpful
suggestions - it is going to take me some time to digest and then try to
implement something - but I will report back and let you know how I am
getting on.
Once again, thanks very much for the h
Dear Colleagues,
The paper
http://dx.doi.org/10.1107/S0108768185002233
in work led by Howard Einspahr undertaken at SRS 7.2 is a protein structural
specific result from synchrotron radiation.
The MAD method of course yielded totally specific to SR protein crystal
structures. The conceptualisati
Adam,
OK, seems like you are going with "it's always statistical error we just
don't yet know what it is" option.
Ed.
On Tue, 2013-03-12 at 16:15 +, Adam Ralph wrote:
> Hi Ed,
>
>
> You can have both types of error in a single experiment, however
> you cannot determine
> statistical
Pete,
> Actually, I was trying to say the opposite - that the decision to
> include something in the model (or not) could change the nature of the
> error.
Duly noted
> Pete
>
> PS - IIUC := ?
>
IIUC - If I Understand Correctly
--
Bullseye! Excellent shot, Maurice.
When I started my PhD (in 1980!) at Imperial, David Blow already had a PhD
student who's project was to use the new Daresbury synchrotron to exploit
anomalous differences. Unfortunately it didn't come on line in time for
him to actually get the data he needed.
I'd be intrigued to know who got the
Yes, this is a key paper demonstrating the possibilities.
The answer to the question of first structure solved is a bit more difficult.
Much of the early use of synchrotrons was for collecting high resolution data
for refinement to supplement data collected on lab sources. This included data
f
Nothing prescient about that. The MAD concept was first proposed by
Herzberg and Lau in 1967, much before sycnhrotrons were used for protein
crystallography.
Herzenberg, A. & Lau, H. S. M. (1967) Acta. Crystallogr. 22, 24-28.
http://scripts.iucr.org/cgi-bin/paper?S0365110X6740
The PNAS p
Herman,
Yes you are right. I was assuming that since these are REMARKs then
programs would ignore them and use the space group in the CRYST1 record to
define the symmetry operators (a better way in my view, assuming that the
space group setting symbol is unambiguous as it should be). If programs
Did anyone see this prescient line in the PNAS paper? Seems that the MAD
concept was suggested way back then...
JPK
"While the enhancement of anomalous scattering
has not yet been examined in detail, it is in principle
possible to use data collected at three wavelengths (15) to
completely solve
Dear Ian,
My feeling is that most crystallograpic programs use indeed a separate
library with symmetry operators acting on fractional coordinates.
However, the SMTRY records in the PDB files work on the orthogonal
coordinates and some of the more advanced non-crystallographic
viewing/modeling pro
Hi James -
If you need the transformed coordinates in the original form for another
program, this may not help, but if you just want to compare the packing between
structures, have a look at PyMOL's matrix_copy command
(http://pymolwiki.org/index.php/Matrix_copy).
# load your files
load file1.
Hi Ian,
You are right, here I was too quick. The orthogonal, not the submitted
coordinates are present in the PDB file. This means that one would indeed need
to transform the SCALE records and either delete or transform the SMTRY records
as well. Leaves the question why one would like to store
In the early days of the PDB coordinates were submitted
in many different coordinate systems:
orthogonal
fractional
grid (normalize each cell edge to 100 so that all coordinates
are between 0 and 100)
build physical model using 2 cm per Angstrom parts and then
measure coordinates
On 13 March 2013 14:51, wrote:
> **
>
> As I see it, there is no need to change the orthogonal coordinates. They
> are used in connection with the SYMTRY records to generate the symmetry
> mates. Changing the orthogonal coordinates would mean changing the SYMTRY
> records, which would only compli
Dear all,
Version 2.7.3 of CCP4MG is now available for download from:
http://www.ccp4.ac.uk/MG/download/
This is a minor bug fix release over the recent 2.7.2
The complete list of changes is give below.
Best wishes,
CCP4MG team.
Changes from 2.7.2:
o Fix Geometry causing crash on Windows/
Hi Herman
Yes your solution would also work, and is also safer in the event that
other programs don't know how to handle SCALE & ORIGX records correctly:
you are just using ORIGX to store the transformation & leave the
co-ordinates alone.
I was imagining that James might want to do further work w
That probably won't be very precise. A better option would be doing an
advanced search, then select Structure Features -> Number of Entities
as a protein query, select "protein" as entity type, and then a very
wide interval starting with 2 (say, between 2 and 100). That returns
14453 hits if I clic
Hi
Not sure if this is strictly speaking the first protein *solved* on a
synchrotron, but I think this is the first report of shooting protein crystals
at a synchrotron in the widely available literature -
http://www.pnas.org/content/73/1/128.full.pdf+html
Phillips J C, Wloda
Dear all,
I want to do a statistics about the number of protein-protein complexes
deposited in PDB in recent years.(1972~1992,1993...2012)
I tried keywords "protein-protein complex", "protein complex" etc. in the
search of PDB but all of them are fail.
Can everyone tell me how to do?
Thank you v
Dear Ian,
As I see it, there is no need to change the orthogonal coordinates. They are
used in connection with the SYMTRY records to generate the symmetry mates.
Changing the orthogonal coordinates would mean changing the SYMTRY records,
which would only complicate things. If we do not change
Hi all - i'm sure this many will know this : when and what was the first
protein structure solved on a synchrotron?
Thanks in advance
Alan
--
Alan Cheung
Gene Center
Ludwig-Maximilians-University
Feodor-Lynen-Str. 25
81377 Munich
Germany
Phone: +49-89-2180-76845
Fax: +49-89-2180-76999
E-mail
Hi James
First off, welcome to CCP4BB!
I think a bit of matrix algebra solves your problem.
Define for the original PDB file:
Xf = SoXo (SCALE transformation orth -> fract).
Xs = OoXo (ORIGX orth -> submitted)
where upper case means matrix or vector, lower case (subscript) identifies
differen
Dear James,
I checked the PDB documentation. Putting the transformation in the ORIGX1,2,3
records should do the trick. However, I wonder if there is any program around
which actually reads and applies the ORIGX1,2,3 transformation. Maybe the
coot/pymol/ccp4mg people could comment? My safest be
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Hash: SHA1
Dear James,
if I understand correctly you want to transform structure B onto
structure A and then compare the crystallographic packing of A and B.
I might be wrong, but I think the most convenient way for the users
would be a display program which can
Dear All,
This is my first post to the group - so "Hello"! I have searched with not much
success to find an answer to my question, so I thought I would try posting here
for some expert advice.
I should start by saying that I am not a crystallographer, but please don't
hold that against me!
Or you can give ccp4mg a go (see the ccp4 website). Makes wonderful
pictures.
(shameless plug from yorkie)
Johan
On 13 March 2013 08:45, wrote:
> **
> Dear Tiantian,
>
> If it is for a picture for a publication, I would use Pymol. I find the
> pictures prettier and you can specify any contour
Ed, sorry for delay. I was not trying to make any significant distinction
between "controllable" and "potentially controllable": from a statistical
POV they are the same thing. The distinction is purely one of
practicality, i.e. within the current experimental parameters is it
possible to elimina
Computational methods development in X-ray crystallography: improved analysis
of potential medicines bound to protein crystals
GlaxoSmithKline (GSK) is a research-based pharmaceutical company with a share
of around 5% of the world's pharmaceutical market and around 13,000 people
actively workin
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Hello!
When you open the display manager and click on "Properties" for the
map in question you find a field where you can type in the contour level.
Regards,
Tim
On 03/13/2013 09:33 AM, ChenTiantian wrote:
> Hi there,
>
> I'm making an OMIT map fig
Dear Tiantian,
If it is for a picture for a publication, I would use Pymol. I find the
pictures prettier and you can specify any contour level you want. If
needed, I can provide you with some commands.
Herman
From: CCP4 bulletin board [mailto:CCP4BB@J
Hi there,
I'm making an OMIT map figure with COOT, and I want to set the contour
level to a specific value, say, 2.0.
Since the initial value is not a whole number, I cannot manage it by
scrolling the wheel. Can I change this value by scripting or something like
that?
Thanks in advance.
--
Tiant
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