Re: [ccp4bb] Fwd: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?

2012-06-06 Thread Michael Thompson 
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 Analysis"

We are lucky to have Richard Dickerson as emeritus faculty here at UCLA, 
because he cares very much for the history of science. Although I do not have a 
personal relationship with him, I always enjoy the opportunity to hear him talk 
about the "beginnings." A couple years ago, we had a symposium to celebrate the 
50th anniversary of the first protein structures with guest speakers including 
Richard Dickerson, David Davies, Brian Matthews, Michael Rossmann, and Bob 
Stroud. Surprisingly, I cannot google my way to a recording of the lectures. 
I'm sure someone got a video or at least an audio recording, so if I can find 
it I will post a link.

Mike T








- Original Message -
From: "Jim Pflugrath" 
To: CCP4BB@JISCMAIL.AC.UK
Sent: Wednesday, June 6, 2012 12:31:56 PM GMT -08:00 US/Canada Pacific
Subject: Re: [ccp4bb] Fwd: [ccp4bb] Fun Question - Is multiple isomorphous 
replacement an obsolete technique?


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] 
Sent: Wednesday, June 06, 2012 2:05 PM 
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Fwd: [ccp4bb] Fun Question - Is multiple isomorphous 
replacement an obsolete technique? 







Begin forwarded message: 



Date: June 6, 2012 3:05:16 PM EDT 

To: aaleshin < 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 Made the Difference: The Growing Power of Anomalous 
Scattering V. 374, pp. 3-22 

Brian Matthews: Transformations in Structural Biology: A Personal View V. 368 
pp. 3-10 

Michael Rossmann: Origins V. 368, pp. 11-21 

Ulrich W. Arndt: Personal X-ray Reflections V. 368, pp. 21-45 

These reminiscences are there entirely because my co-Editor Bob Sweet felt 
exactly the same way Alex does. 

Charlie 

On Jun 6, 2012, at 2:12 PM, aaleshin wrote: 



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 
... 

-- 
Michael C. Thompson

Graduate Student

Biochemistry & Molecular Biology Division

Department of Chemistry & Biochemistry

University of California, Los Angeles

mi...@chem.ucla.edu

Re: [ccp4bb] Fwd: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?

2012-06-06 Thread Jim Pflugrath 
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]
Sent: Wednesday, June 06, 2012 2:05 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Fwd: [ccp4bb] Fun Question - Is multiple isomorphous 
replacement an obsolete technique?



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 Made the Difference:  The Growing Power of Anomalous 
Scattering V. 374, pp. 3-22

Brian Matthews:  Transformations in Structural Biology:   A Personal View  V. 
368 pp. 3-10

Michael Rossmann:  Origins V. 368, pp. 11-21

Ulrich W. Arndt:  Personal X-ray Reflections  V. 368, pp. 21-45

These reminiscences are there entirely because my co-Editor Bob Sweet felt 
exactly the same way Alex does.

Charlie

On Jun 6, 2012, at 2:12 PM, aaleshin wrote:

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
...

[ccp4bb] Fwd: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?

2012-06-06 Thread Carter, Charlie 


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 Made the Difference:  The Growing Power of Anomalous 
Scattering V. 374, pp. 3-22

Brian Matthews:  Transformations in Structural Biology:   A Personal View  V. 
368 pp. 3-10

Michael Rossmann:  Origins V. 368, pp. 11-21

Ulrich W. Arndt:  Personal X-ray Reflections  V. 368, pp. 21-45

These reminiscences are there entirely because my co-Editor Bob Sweet felt 
exactly the same way Alex does.

Charlie

On Jun 6, 2012, at 2:12 PM, aaleshin wrote:

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 Bricogne wrote:

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 1973-74. The data were
collected at room temperature on a rotating-anode source, using film on an
Arndt-Wonacott rotation camera (the original prototype!). The films were
scanned on a precursor of the Optronics scanner, and the intensities were
integrated and scaled with the early versions of the Rotavata and Agrovata
programs (mention of which should make many ccp4 old-timers swoon with
nostalgia). 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. This contributed very substantially to the phasing of the
structure.

  In fact it would be a healthy exercise to RTFL (Read The Fascinating
Literature) in this area, in particular the beautiful 1966 papers by Brian
Matthews in Acta Cryst. vol 20, to see how seriously anomalous scattering
was already taken as a source of phase information in macromolecular
crystallography in the 1960's.

  In spite of that, of course, there would always be the unhappy cases
where the anomalous differences were too noisy, or the data processing
program too unsophisticated to filter them adequately, so that only the
isomorphous differences would be useful. It was in order to carry out such
filtering that Brian Matthews made another crucial contribution in the form
of the Local Scaling method (Acta Cryst. A31, 480-487).


  With best wishes,

   Gerard.

--
On Wed, Jun 06, 2012 at 11:02:05AM -0400, 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 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. Therefore MIR was needed. Also, current 
hardware/software
produces much better reduced data, so weak signals can become useful.

Fred

***
Fred Dyda, Ph.D.   Phone:301-402-4496
Laboratory of Molecular BiologyFax: 301-496-0201
DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov
Bldg. 5. Room 303
Bethesda, MD 20892-0560  URGENT message e-mail: 
2022476...@mms.att.net
Google maps coords: 39.000597, -77.102102
http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred
***

--

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