Dear All,
I want to use dash line to present the salt bridge in a crystal structure in
the paper publication, for example the salt bridge formed between Glu (OE1 and
OE2) and Lys (terminal N).
Do you suggest I only draw a single dashed line between the terminal N of the
Lys and the closer ato
I'm afraid I seriously mistrust the sigma and e/A^3 numbers reported
by Coot for ncs averaged maps. I work with a crystal with near perfect
6-fold ncs and the e/A^3 numbers make no sense. For a 2Fo-Fc style map
the e/A^3 values should be nearly the same after as before. They are not.
The
Hi Ivan,
I'm not sure which version of phenix you are using, but in 1.7.3-928 GUI
restraints are generated for metals using the "ReadySet". ReadySet creates a
file called your_pdb_file_name.metal.edits. The file I generated gave standard
deviations to bond lengths of 0.05-0.25.
Prior to gener
ohh this is a passive stereo projector. what's the distance from the
projector to the screen?
On Wed, Jun 6, 2012 at 6:37 PM, Min, Xiaoshan wrote:
> Hi CCP4,
>
> I am curious if anyone has setup 3D-projector for large conference room. We
> have a LG CF3D projector and it is coupled to a Linux
Hi CCP4,
I am curious if anyone has setup 3D-projector for large conference room. We
have a LG CF3D projector and it is coupled to a Linux machine with Nvidia
Quadro FX 3800. We haven't been able to get 3D working. If someone has
experience with this projector, could you share the setting on
On 06/06/12 21:47, Ursula Schulze-Gahmen wrote:
I calculated threefold averaged omit maps in coot. These maps look
nice and clean, but I am having trouble making sense of the displayed
sigma levels or e/A3 values. When I display the unaveraged and
averaged maps at a similar density level for th
Ursula,
please don't forget that you are looking at Fourier image of electron
density distribution, which may be as different from the true electron
density distribution as different from zero the F000 reflection and as
different your Fobs data set from being 100% complete for all possible
reflect
I can only confirm what Alex said. And the structure was neither a
globin or zyme or psin!
Victor
Quoting aaleshin :
I and Victor Lamzin solved our first protein structure (3A
resolution) in 80-s using pure MIR and a home made (Russian)
diffractometer...
Alex
On Jun 6, 2012, at 1:42 P
I and Victor Lamzin solved our first protein structure (3A resolution) in 80-s
using pure MIR and a home made (Russian) diffractometer...
Alex
On Jun 6, 2012, at 1:42 PM, Boaz Shaanan wrote:
> So if get the gist of the thread right, am I correct in assuming that the
> last protein structures t
MIRAS doesn't count, only MIR (If I understand the original question correctly).
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220 Skype: boaz.shaanan
Fax: 972-8-647-2992 or 972-8
No, I listed a few recent ones
V. Gaur, et al., Plant Physiol., 152(4), 1842-1850 (2010)
O. Antipova, J Biol Chem. 2010 Mar 5;285(10):7087-96. Epub 2010 Jan 6.
Y. Nakajima, J Bacteriol. 2008 Dec;190(23):7819-29. Epub 2008 Sep 26.
S. Stayrook, Nature. 2008 Apr 24;452(7190):1022-5.
Many MIRAS,
So if get the gist of the thread right, am I correct in assuming that the last
protein structures to be solved strictly by MIR are haemoglobin/myoglobin,
lysozyme and chymotrypsin and perhaps one or two more in the late sixties? In
which case the answer to the original question about MIR being
While neither of these references detail the "development" of protein
crystallography, they are excellent stories of its birth:
1.) A book written by Richard Dickerson, "Present at the flood"
2.) A recent review in JMB by Strandberg, Dickerson, and Rossmann: "50 years of
Protein Structure Analy
Given Cu, yes, the five M edges between 2.3keV and 3.6keV contribute a
continuum transition signal of the 8e- you initially referred to.
-Original Message-
From: Jacob Keller [mailto:j-kell...@fsm.northwestern.edu]
Sent: Wednesday, June 06, 2012 12:35 PM
To: b...@hofkristallamt.org
Cc:
It would be helpful if I finished my own sentences. As an aside for those
who feel that capillary mounting is a lost art among the newer generation I
assure you it isn't. All you need is a busted cryo system and a crystal
backlog to get past the intimidation factor.
Katherine
On Wed, Jun 6, 2012
>From personal and recent experience I've solved a structure using only
iodine anomalous at Cu K-alpha from a RT crystal (a capillary mounted one
at that). The anomalous signal from iodine is surprisingly robust on a home
source even at room temp.
Katherine
As an aside for those who feel that cap
I calculated threefold averaged omit maps in coot. These maps look nice and
clean, but I am having trouble making sense of the displayed sigma levels
or e/A3 values. When I display the unaveraged and averaged maps at a
similar density level for the protein the unaveraged map is at 0.024 e/A3
and 2.
Just for clarification: I didn't try to claim that there was no anomalous
signal, simply that in some cases it was difficult use it, because the
data weren't that great.
fred
[32m***
Fred Dyda, Ph.D.
Dear Jacob,
What I meant was that I thought it was a pleasant surprise to see
that there was enough anomalous signal at all in these noisy data
(which were collected from several crystals, suffering from radiation
damage at room temperature, from sizeable absorption effects etc.) to
get a ref
But the edges for I and Hg are pretty far from CuKa (see attached). I
am familiar with their being extra signal (white lines) very close to
the peak, but not so far away
JPK
On Wed, Jun 6, 2012 at 2:15 PM, Bernhard Rupp (Hofkristallrat a.D.)
wrote:
> There is also a relevant point from the
And for more Personal Reflections, one may wish to take a gander at the Rigaku
Webinar series with presentations by Brian Matthews and Michael G. Rossmann.
Jim
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Carter, Charlie
[car...@med.unc.edu]
S
===
SYNCHROTRON BEAM TIME FOR MACROMOLECULAR CRYSTALLOGRAPHY AT SLS
===
Proposal application deadline: Friday, June 15, 2012
Periods:
September 1, 2012 - Decem
There is also a relevant point from the physics of the absorption spectra -
the XANES white lines (near edge peaks higher than the continuum transition
or edge step) depend on the chemical environment of the anomalous atom in
terms of available unoccupied states (which n. b. is something entirely
d
Begin forwarded message:
Date: June 6, 2012 3:05:16 PM EDT
To: aaleshin mailto:aales...@burnham.org>>
Subject: Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an
obsolete technique?
There are four such papers in Methods in Enzymology, Vols 368 and 374:
David Blow: How Bijvoet
Richard Dickerson's book is relevant and gripping reading
http://www.amazon.com/gp/product/0878931686?ie=UTF8&tag=brscrystallot-20&lin
kCode=as2&camp=1789&creative=9325&creativeASIN=0878931686
BR
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
a
No offense taken (we all have our dour moments!), but grant me a
sincere question: the f" occupancy value would have been just as close
at 11 as 5 if the true value were 8, am I correct? In other words, do
you imply by saying "doing well" that you got as *much* as 5, or that
you got as *close* as 5
I wonder if anyone attempted to write a historic book on development of
crystallography. That generation of crystallographers is leaving this world and
soon nobody will be able to say how the protein and non-protein structures were
solved in those days.
Alex
On Jun 6, 2012, at 8:48 AM, Gerard
Dear Jacob and all,
I realise that my last statement sounds awfully dour and dismissive, in
a way I really didn't intend. Especially as Stefan's original posting was a
"Fun Question".
Apologies to all for this over-the-top statement. I enjoyed a lot of
the replies.
With
A postdoctoral position is available at the University of Maryland,
Baltimore, in the Department of Pharmaceutical Sciences.
Prior experience in crystallography is NOT required, only willingness to
learn the method. Strong background in molecular biology techniques
and/or biophysical methods will
Dear Jacob,
I thought that getting 5 for each iodine was doing pretty well, given
the circumstances - e.g. the noisy measurements, the primitive software
running on slow computers with tiny amounts of memory, etc. .
In any case my main point, directed at the original poster, was that
r
...Even with such primitive techniques, I can remember an HgI4
> derivative in which you could safely refine the "anomalous occupancies"
> (i.e. f" values) for the iodine atoms of the beautiful planar HgI3 anion to
> 5 electrons.
I am surprised--f"'s of I and Hg are supposed to be around 8 for CuK
Remember that it's all relative to the length of the FP vector. If your FP
vector is small, then the f" component can substantially change the phase,
even with a small f" component. So if you have measured a number of
relatively weak reflections with minimal error, there is a substantial
anomalous
Dear Fred,
May I join Phil Evans in trying to dissipate the feeling that anomalous
differences were fictional before flash-freezing and all the mod cons. I can
remember cutting my teeth as a PhD student by helping Alan Wonacott with the
experimental phasing of his B.St. GAPDH structure in 197
Once again I wanted to draw everyone's attention to the
Cold Spring Harbor Laboratory 2012 X-ray Methods in Structural Biology
course which will take place
October 15 through October 30, 2012.
The official course announcement is here:
http://meetings.cshl.edu/courses/c-crys12.shtml
I think the
Even today, we still try to soak existing native protein crystals with heavy
atoms at the same time while SeMet substituted protein is prepared.
Nearly half of the times, we are able to solve the structure with HA (always
SIRAS) before we have the SeMet protein.
A recent example:
Structure. 200
Bijvoet - 1949 !
FF
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
I think some have used anomalous signals since the 1930s-40s, e.g., Bijvoet!
JPK
On Wed, Jun 6, 2012 at 10:23 AM, Ronald E Stenkamp
wrote:
> There were a number of labs using anomalous dispersion for phasing 40 years
> ago. The theory for using it dates from the 60s. And careful experimental
>
There were a number of labs using anomalous dispersion for phasing 40 years
ago. The theory for using it dates from the 60s. And careful experimental
technique allowed the structure solution of several proteins before 1980 using
what would be labeled now as SIRAS. Ron
On Wed, 6 Jun 2012, Dy
Anomalous signal even with room temperature capillary data was measurable on
diffractometers and early area detectors.
However there were misspellings in software packages such as sending anomalous
phase 90deg into the wrong direction
in one of them or others.
After in-house editing, anomalous
> I suspect that there was a time when the anomalous signal in data sets was
> fictional.
> Before the invent of flash freezing, systematic errors due to decay and the
> need
> of scaling together many derivative data sets collected on multiple crystals
> could render
> weak anomalous signal use
No they were not useless! I used them
(probably better now with cryo data though)
Phil
On 6 Jun 2012, at 16:02, Dyda wrote:
>> I suspect that pure MIR (without anomalous) was always a fiction. I doubt
>> that anyone has ever used it. Heavy atoms always give
>> an anomalous signal
>
>> Phil
>
>I suspect that pure MIR (without anomalous) was always a fiction. I doubt that
>anyone has ever used it. Heavy atoms always give
>an anomalous signal
>Phil
I suspect that there was a time when the anomalous signal in data sets was
fictional.
Before the invent of flash freezing, systematic erro
One could consider RIP (phasing using radiation induced damage) as SIR
technique. At short wavelengths ( Hey!
>
> I was just wondering, do you know of any recent (~10y) publication
that presented a structure solution solely based on MIR? Without the
use of any anomalous signal of some sort?
>
I suspect that pure MIR (without anomalous) was always a fiction. I doubt that
anyone has ever used it. Heavy atoms always give an anomalous signal
Phil
On 6 Jun 2012, at 03:55, Stefan Gajewski wrote:
> Hey!
>
> I was just wondering, do you know of any recent (~10y) publication that
> presen
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