]
Sent: Wednesday, June 13, 2012 3:47 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an
obsolete technique?
I think there is a misconception floating around that processing your
data with anomalous turned on will somehow degrade the quality
@JISCMAIL.AC.UK] on behalf of James Holton
[jmhol...@lbl.gov]
Sent: Wednesday, June 13, 2012 3:47 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an
obsolete technique?
I think there is a misconception floating around that processing your
Why would anyone ignore the anomalous data they had collected? It will always
help the phasing, and decide the hand for you..
Eleanor
On 6 Jun 2012, at 03:55, Stefan Gajewski wrote:
Hey!
I was just wondering, do you know of any recent (~10y) publication that
presented a structure
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
I suspect that there was a time when the anomalous signal in data sets was
fictional.
Before the invent of flash freezing, systematic errors
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
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 useless.
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
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,
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
stenk...@u.washington.edu wrote:
There were a number of labs using anomalous dispersion for phasing 40 years
ago. The theory for using it dates from the 60s.
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
bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ronald
E Stenkamp
Sent: Wednesday, June 06, 2012 10:23 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an
obsolete technique?
There were a number of labs using anomalous dispersion for phasing
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
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
...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 CuKa
(or
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
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
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,
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?
Of
aaleshin
Sent: Wednesday, June 06, 2012 11:12 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an
obsolete technique?
I wonder if anyone attempted to write a historic book on development of
crystallography. That generation of crystallographers
Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jacob
Keller
Sent: Wednesday, June 06, 2012 11:30 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an
obsolete technique?
No offense taken (we all have our dour moments
-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jacob
Keller
Sent: Wednesday, June 06, 2012 11:30 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an
obsolete technique?
No offense taken (we all have our dour moments
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
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.
: [ccp4bb] Fun Question - Is multiple isomorphous replacement
an
obsolete technique?
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
evidence (scan) might want to consider that.
Best, BR
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Jacob
Keller
Sent: Wednesday, June 06, 2012 11:30 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Fun Question - Is multiple
: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an
obsolete technique?
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
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Phil Evans
[p...@mrc-lmb.cam.ac.uk]
Sent: Wednesday, June 06, 2012 6:04 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an
obsolete technique?
No they were
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,
-8-646-1710
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Santarsiero,
Bernard D. [b...@uic.edu]
Sent: Wednesday, June 06, 2012 11:46 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement
Evans
[p...@mrc-lmb.cam.ac.uk]
Sent: Wednesday, June 06, 2012 6:04 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an
obsolete technique?
No they were not useless! I used them
(probably better now with cryo data though)
Phil
or 972-8-646-1710
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Phil
Evans [p...@mrc-lmb.cam.ac.uk]
Sent: Wednesday, June 06, 2012 6:04 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Fun Question - Is multiple isomorphous
On Tuesday, 05 June 2012, Stefan Gajewski wrote:
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?
A text search for MIR returns 1377 PDB structures overall.
33 matches
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