[ccp4bb] Faculty position at the University of Kentucky

[Young-In Chi]

As seen in the 25 May issue of Science:

Dream. Challenge. Succeed
BIOCHEMISTRY FACULTY POSITION

The Department of Molecular and Cellular Biochemistry invites applications 
for a tenure track faculty position at the Assistant Professor level. The 
successful candidate must possess a Ph.D., M.D. or equivalent degree and 
have an active research program using structural methods to address 
questions of biomedical relevance. We are particularly interested in 
candidates that use X-ray crystallography as their major technique and whose 
research interests complement existing departmental programs including, but 
not limited to the areas of diabetes, cardiovascular disease, neuroscience, 
and cancer research. Preference will be given to candidates with a proven 
record of scholarly achievement in structural biology


The successful candidate will benefit from a stimulating and collaborative 
environment within the department and a strong graduate program. Competitive 
start-up funds, salaries, state-of-the-art facilities including equipment 
for X-ray crystallography, access to the SER-CAT beamline at the Advanced 
Photon Source and appropriate space will be offered in a new 185,000 ft2 
research building


Evaluation of applicants will begin July 2007. Please email your application 
materials, a curriculum vitae and a description of your current and future 
research program. Candidates should also submit three references via email 
or mail to:


MCBX Faculty Search Committee
Email: [EMAIL PROTECTED]
B278 Biomed. Biol. Sc. Res. Bldg
741 South Limestone St
Lexington, KY 40536-0509

For further information about the Department,
visit: http://www.mc.uky.edu/biochemistry

The University of Kentucky is an equal opportunity employer
and encourages applications from minorities and women

[ccp4bb] Position opening at RCSB PDB/Rutgers University- BIOCHEMICAL INFORMATION & ANNOTATION SPECIALIST

[Jasmine Young]

The RCSB Protein Data Bank (http://www.pdb.org) is a publicly accessible 
information portal for researchers and students interested in structural 
biology. At its center is the PDB archive -- the sole international 
repository for the 3-dimensional structure data of biological 
macromolecules. These structures hold significant promise for the 
pharmaceutical and biotechnology industries in the search for new drugs 
and in efforts to understand the mysteries of human disease


The primary mission of the RCSB PDB is to provide accurate, 
well-annotated data in the most timely and efficient way possible to 
facilitate new discoveries and scientific advances. The RCSB processes, 
stores, and disseminates these important data, and develops the software 
tools needed to assist users in depositing and accessing structural 
information


The RCSB Protein Data Bank at Rutgers University in Piscataway, NJ has 
an opening for a Biochemical Information & Annotation Specialist to 
curate and standardize macromolecular structures for distribution in the 
PDB archive. The annotation specialist communicates daily with members 
of the deposition community, and annotates, releases, and updates 
entries in the PDB archive. BLAST, PubMed, and other tools are used for 
the annotation process performed on a linux box


We have multiple positions opening. A background in cryo-electron 
microscopy or small molecule crystallography or macromolecular 
crystallography is a strong advantage. Biological chemistry (PhD, MS, BS 
or BA) is required. Experience with linux computer systems, biological 
databases is preferred. The successful candidate should be 
self-motivated, pay close attention to detail, possess strong written 
and oral communication skills, and meet deadlines


This position offers the opportunity to participate in an exciting 
project with significant impact on the scientific community


Please send resume (pdf preferred) to Dr. Helen M. Berman at 
[EMAIL PROTECTED]

[ccp4bb] Position opening at RCSB PDB/Rutgers University- BIOCHEMICAL INFORMATION & ANNOTATION SPECIALIST

[Jasmine Young]

The RCSB Protein Data Bank (_http://www.pdb.org _) 
is a publicly accessible information portal for researchers and students 
interested in structural biology. At its center is the PDB archive -- 
the sole international repository for the 3-dimensional structure data 
of biological macromolecules. These structures hold significant promise 
for the pharmaceutical and biotechnology industries in the search for 
new drugs and in efforts to understand the mysteries of human disease


The primary mission of the RCSB PDB is to provide accurate, 
well-annotated data in the most timely and efficient way possible to 
facilitate new discoveries and scientific advances. The RCSB processes, 
stores, and disseminates these important data, and develops the software 
tools needed to assist users in depositing and accessing structural 
information


The RCSB Protein Data Bank at Rutgers University in Piscataway, NJ has 
an opening for a Biochemical Information & Annotation Specialist to 
curate and standardize macromolecular structures for distribution in the 
PDB archive. The annotation specialist communicates daily with members 
of the deposition community, and annotates, releases, and updates 
entries in the PDB archive. BLAST, PubMed, and other tools are used for 
the annotation process performed on a linux box


A background in cryo-electron microscopy is a strong advantage. 
Biological chemistry (PhD, MS, BS or BA) is required. Experience with 
linux computer systems, biological databases is preferred. The 
successful candidate should be self-motivated, pay close attention to 
detail, possess strong written and oral communication skills, and meet 
deadlines


This position offers the opportunity to participate in an exciting 
project with significant impact on the scientific community


Please send resume (pdf preferred) to Dr. Helen M. Berman at 
[EMAIL PROTECTED] 
_ 

Re: [ccp4bb] Is anomalous signal a different wavelength?

[marc . schiltz]

Quoting Jacob Keller <[EMAIL PROTECTED]>:

The reason I called the phenomenon "resonant scattering" is because   
that is the term used by
"Elements of Modern X-ray Physics" by Jens Als-Nielsen, Des   
McMorrow. I prefer the term also
because this scattering is, as somebody has said, no longer really   
"anomalous--" it fits well into

x-ray physical theory.




Let the heroes speak:

In 1994 D. H. Templeton wrote:

"The index of refraction of transparent materials for visible light  
generally increases as the wavelength decreases and this dispersion is  
said to be 'normal'. Near absorption bands there are intervals of  
wavelength where the slope of n versus \lambda is positive, and the  
dispersion is 'anomalous'. According to this convention and the  
relation between n and f', x-ray dispersion is anomalous only in those  
intervals where df'/d\lambda is negative. Yet 'anomalous dispersion'  
and 'anomalous scattering' have come to be used for the effects of  
absorption on x-ray optical properties at all wavelengths, or  
sometimes perhaps only for those related to the imaginary term f".  
These effects are significant for nearly all atoms at all wavelengths  
commonly used for diffraction experiments, and therefore 'anomalous'  
is somewhat inappropriate. I prefer 'dispersion' or 'resonant  
scattering'."


(in 'Resonant Anomalous X-ray Scattering: Theory and Applications',  
G.Materlik, C.J.Sparks & K.Fischer (eds.), Elsevier Science,  
Amsterdam: 1994)



The editors (G.Materlik, C.J.Sparks & K.Fischer) of that same book  
wrote in the preface:


"Since resonant interactions are characteristic of the interaction of  
photons with matter, we suggest that 'resonant' better describes the  
field than 'anomalous' scattering."


But note that they used the pleonasm "Resonant Anomalous X-ray  
Scattering" as a title for their book ;-)



More recent review articles use the term "resonant" scattering or  
"resonant" diffraction, e.g.


Hodeau JL, Favre-Nicolin V, Bos S, Renevier H, Lorenzo E, Berar JF  
(2002). "Resonant diffraction". Chem Rev. 101, 1843--1867.


which includes a section on MAD phasing.


Thus, "resonant scattering" and "anomalous scattering" are synonyms  
and it is almost a matter of taste which term one prefers. Both are  
perfectly acceptable. The x-ray physics and crystallography  
communities (except protein crystallography) have shifted from the  
usage of "anomalous scattering" to "resonant scattering".


But then, as you write, if we want to keep the MAD SAD SIRAS etc  
acronyms we are tied to "anomalous".




Marc Schiltz

[ccp4bb] anomalous signal

[Yves Muller]

ps perhaps "anomalous" is better than "resonant," as it produces "MAD" and "SAD" and not 
"MRD" and
"SRD"...


MRD would indeed be a poor name. For French scientists it might be difficult to 
get funding for an MRD experiment
Regards
Yves


--

Prof. Yves Muller   Phone: +49-(0)-9131-8523082, 8523081
Lehrstuhl fuer BiotechnikFAX:   +49-(0)-9131-8523080
www.biologie.uni-erlangen.de/biotechnik 
Institut fuer Biologie

Friedrich-Alexander-Universität, Erlangen-Nuernberg
Im IZMP, Henkestrasse 91, D-91052 Erlangen  

Re: [ccp4bb] Is anomalous signal a different wavelength?

[Jacob Keller]

Dear Crystallographers,

The reason I called the phenomenon "resonant scattering" is because that is the 
term used by
"Elements of Modern X-ray Physics" by Jens Als-Nielsen, Des McMorrow. I prefer 
the term also
because this scattering is, as somebody has said, no longer really 
"anomalous--" it fits well into
x-ray physical theory.

As for Compton scattering, I was under the impression that the event was a free 
electron being
perturbed back and forth by an incoming EM wave, which changes its velocity, 
and like an free
electron/positron bouncing around a synchrotron, the perturbed electron 
releases a photon, which
emerges as a spherical wave. This spherical wave then is able to interact with 
all other
spherical-wave photons emerging from analogous electrons elsewhere in the 
crystal. (Would this mean 
all of the constructively-interfering electron wave-functions would have to be 
in phase with each
other, in the whole crystal? A conundrum...)

Concerning resonant scattering, it seemed to me that the lower-level k- or 
l-edge (not free)
electron was excited to a higher state, and another electron dropped down to 
fill its place. This
process would on average take a finite amount of time, inducing an absolute 
phase shift in its
emerging spherical wave, relative to the regular Compton-scattered wave. This 
phase shift is
modelled by two vectors, real and imaginary, in complex space, which together 
represent the phase
shift. No matter the phase of the protein wave, the length and direction of 
these vectors stays the 
same at a given wavelength. When the wavelength is shifted, say to the F' 
minimum (inflection), the 
average time required for the resonant scattering event changes, resulting in a 
different absolute
phase shift which is little shifted from the Compton-scattered wave, although 
it might be even a
few periods behind. I will try to look into this, and see if the observations 
and equations agree
with what I am saying.

All the best,

Jacob Keller

ps perhaps "anomalous" is better than "resonant," as it produces "MAD" and 
"SAD" and not "MRD" and
"SRD"...


==Original message text===
On Thu, 31 May 2007 11:57:21 am CDT William Scott wrote:

Dear Fellow Compatriots:

A few pre-coffee random observations from the field offices of Dr. Cranky:

1. No mention of "Resonant Scattering in the index of JJ Sakurai Adv.
Quantum Mechanics (1967, 1987 revision), which I used in (blush) 1989,
although the phenomenon is discussed, with many exercises left to the
reader. The index did, however, refer to the "retarded Green's function,"
which I find delightful in this context.

2.  "Resonance scattering" does appear in JJ Sakurai, Modern Quantum
Mechanics, which is a book he wrote a little bit later, and published in
1985 after he died. So I guess that dates the term as well as me.

3. "Anomalous scattering" in optics (i.e, the same phenomenon) describes
the __inversion__ of the rainbow spectrum (dispersion) when white light
propagates through a prism in which there are absorbers that absorb light
near to the visible spectrum. This is accounted for with an imaginary
component in the index of refraction. So violet is where you would
normally expect to see red, and vice versa.

4. The QM analogue takes as its starting point the First Born
approximation (I'm too tired to make a pun) in which a single photon
scatters once elastically from a billiard ball point scattering center.
You can then show that the diffraction pattern is the FT of the potential,
and then get it into the form of electron density from there. Anomalous
scattering dispersion and absorption effects are essentially grafted on as
real and imaginary terms in the denominator of the scattering potential
(see retarded Green's function, above). What comes out of that treatment
is essentially identical to what you have in that equation in James that
Blundell and Johnson use as a starting point for the derivation. The main
point is it is phase shifting. The photon frequency is not changed.

5. Resonance scattering requires a different sort of potential in which
you have what Sakurai calls a "quasi-bound state" with a soft barrier. 
The energy barrier has to be of the same order as the energy of the
photon, so I think for X-rays this isn't a significant effect.


 Bill Scott
===End of original message text===



***
Jacob Keller
Northwestern University
6541 N. Francisco #3
Chicago IL 60645
(847)467-4049
[EMAIL PROTECTED]
***

[ccp4bb] density modification

[Gina Clayton]

Hi CCP4ers

firstly apologies that this is slighty off ccp4 topic but does  anyone know of a
programme whereby I can use solvent flipping with multi domain  masks in
addition to a solvent mask for my phases i.e. not based on a model?  I
wanted to use CNS density_modify (my maps are currently from DM multi -uses
 solvent
flattening) but DM in CNS  accepts only one mask. So I guess my  real
question,which is why it is off topic, does anyone know of a way of 
successfully modifying density_modify to get it to accept multi masks or an
alternative (other than resolve)?"


thanks for any advice in advance!

Gina

Re: [ccp4bb] Is anomalous signal a different wavelength?

[William Scott]

Dear Fellow Compatriots:

A few pre-coffee random observations from the field offices of Dr. Cranky:

1. No mention of "Resonant Scattering in the index of JJ Sakurai Adv.
Quantum Mechanics (1967, 1987 revision), which I used in (blush) 1989,
although the phenomenon is discussed, with many exercises left to the
reader. The index did, however, refer to the "retarded Green's function,"
which I find delightful in this context.

2.  "Resonance scattering" does appear in JJ Sakurai, Modern Quantum
Mechanics, which is a book he wrote a little bit later, and published in
1985 after he died. So I guess that dates the term as well as me.

3. "Anomalous scattering" in optics (i.e, the same phenomenon) describes
the __inversion__ of the rainbow spectrum (dispersion) when white light
propagates through a prism in which there are absorbers that absorb light
near to the visible spectrum. This is accounted for with an imaginary
component in the index of refraction. So violet is where you would
normally expect to see red, and vice versa.

4. The QM analogue takes as its starting point the First Born
approximation (I'm too tired to make a pun) in which a single photon
scatters once elastically from a billiard ball point scattering center.
You can then show that the diffraction pattern is the FT of the potential,
and then get it into the form of electron density from there. Anomalous
scattering dispersion and absorption effects are essentially grafted on as
real and imaginary terms in the denominator of the scattering potential
(see retarded Green's function, above). What comes out of that treatment
is essentially identical to what you have in that equation in James that
Blundell and Johnson use as a starting point for the derivation. The main
point is it is phase shifting. The photon frequency is not changed.

5. Resonance scattering requires a different sort of potential in which
you have what Sakurai calls a "quasi-bound state" with a soft barrier. 
The energy barrier has to be of the same order as the energy of the
photon, so I think for X-rays this isn't a significant effect.


 Bill Scott

Re: [ccp4bb] Rfree into an existing mtz...

[Patskovsky Yury]

Hi James,
F2mtz will do it.


On Thu, 31 May 2007, James Pauff wrote:


Good day all,

What is the best means of getting a freeR column into
an existing mtz file?  I've noticed the "Edit MTZ"
command bar in CCP4, but there are other options (such
as conversion to XPLOR and then back to MTZ) that seem
to be able to accomplish the same thing, although
there appear to be changes in the reflection
parameters upon this conversion.

Basically, I just want to add a freeR column to
monitor my refinement(s).

Thank you as usual.



Looking
 for a deal? Find great prices on flights and hotels with Yahoo! FareChase.
http://farechase.yahoo.com/

Re: [ccp4bb] Is anomalous signal a different wavelength?

[Ethan A Merritt]

On Thursday 31 May 2007 01:37, Marc SCHILTZ wrote:
> Ethan A Merritt wrote:
> > And please note that "resonant scattering" is not a standard term.   
> 
> "Resonant Scattering" is now the standard term accepted and used 
> anywhere in the X-ray physics and crystallography literature, except in 
> protein crystallography.

I stand corrected.

Is there a IUPAC or other standard definition of the term?
My attempts to find one via Google did not turn up anything definitive.

The literature examples that I found use the term to refer to the experiment
itself, or to the scattering process as a whole. However the original
poster used the term in such a way that made it sound as if the
"resonant scattering" was roughly a synonym for "imaginary component of the
scattering factor", which is not exactly the same thing. If we protein
crystallographers are to begin using the term, we should first pin down
what the definition is.

> It is the more adequate term since the X-ray phenomena under discussion 
> involve resonant interactions of photons with matter and are actually 
> not at all 'anomalous'.

The 'anomalous' behaviour that gave rise to this label is the violation
of the general principle that the strength of interaction between
light and solid matter decreases as the wavelength decreases.
At an absorption edge, the scattering curve is anomalous because
the strength of the interaction is not monotone decreasing with photon energy.
Instead it increases as you approach the edge from either direction.
The term was inherited from the description of experiments with visible
light that characterized the wavelength-dependence of a material's index of
refraction.


-- 
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742

Re: [ccp4bb] refmac crashes when ncs restraints are applied

[Eleanor Dodson]

I certainly have used NCS restraints with ccp4-6.0.2
That doesnt help much though does it!
Eleanor

[EMAIL PROTECTED] wrote:

Date: Thu, 31 May 2007 14:57:03 +0100
From: Stephen Brian Carr <[EMAIL PROTECTED]>
To: ccp4bb@jiscmail.ac.uk
Subject: refmac crashes when ncs restraints are applied
Message-ID: 
MIME-Version: 1.0
Content-Type: TEXT/PLAIN; charset=US-ASCII


Dear CCP4 users,

I am running refmac 5.2.0019 in ccp4 6.0.2 on a model that contains four
monomers per asymmetric unit. The resolution of the data is 2.5 Angstrom
so I want to apply ncs restraints.  When I define each chain
as an ncs group in refmac and attempt to run a refinement the program
crashes with the message

#CCP4I TERMINATION STATUS 0 child killed: segmentation violation
#CCP4I TERMINATION TIME 30 May 2007  15:49:42
#CCP4I MESSAGE Task failed

looking at the log file suggests that the program had only read in the
pdb file and done nothing else before crashing.

Refinement runs without ncs restraints runs fine, also running an
identical job in ccp4 6.0.1 (refmac 5.2.0019) with ncs restraints also
runs fine.

Has anyone else come across this problem?

I am operating on a linux PC running Suse 10.2

Thanks very much in advance for any suggestions as to how to get around
this.

Steve Carr


  

[ccp4bb] refmac crashes when ncs restraints are applied

[bmbsbc]

Date: Thu, 31 May 2007 14:57:03 +0100
From: Stephen Brian Carr <[EMAIL PROTECTED]>
To: ccp4bb@jiscmail.ac.uk
Subject: refmac crashes when ncs restraints are applied
Message-ID: 
MIME-Version: 1.0
Content-Type: TEXT/PLAIN; charset=US-ASCII


Dear CCP4 users,

I am running refmac 5.2.0019 in ccp4 6.0.2 on a model that contains four
monomers per asymmetric unit. The resolution of the data is 2.5 Angstrom
so I want to apply ncs restraints.  When I define each chain
as an ncs group in refmac and attempt to run a refinement the program
crashes with the message

#CCP4I TERMINATION STATUS 0 child killed: segmentation violation
#CCP4I TERMINATION TIME 30 May 2007  15:49:42
#CCP4I MESSAGE Task failed

looking at the log file suggests that the program had only read in the
pdb file and done nothing else before crashing.

Refinement runs without ncs restraints runs fine, also running an
identical job in ccp4 6.0.1 (refmac 5.2.0019) with ncs restraints also
runs fine.

Has anyone else come across this problem?

I am operating on a linux PC running Suse 10.2

Thanks very much in advance for any suggestions as to how to get around
this.

Steve Carr

[ccp4bb] refmac crashes when ncs restraints applied

[bmbsbc]

Date: Thu, 31 May 2007 14:38:42 +0100
From: Stephen Brian Carr <[EMAIL PROTECTED]>
To: [EMAIL PROTECTED]
Subject: refmac crashes when ncs restraints applied
Message-ID: 
MIME-Version: 1.0
Content-Type: TEXT/PLAIN; charset=US-ASCII


Dear CCP4 users,

I am running refmac 5.2.0019 in ccp4 6.0.2 on a model that contains four 
monomers per asymmetric unit. The resolution of the data is 2.5 Angstrom 
so I want to apply ncs restraints.  When I define each chain 
as an ncs group in refmac and attempt to run a refinement the program 
crashes with the message

#CCP4I TERMINATION STATUS 0 child killed: segmentation violation
#CCP4I TERMINATION TIME 30 May 2007  15:49:42
#CCP4I MESSAGE Task failed

looking at the log file suggests that the program had only read in the 
pdb file and done nothing else before crashing.

Refinement runs without ncs restraints runs fine, also running an 
identical job in ccp4 6.0.1 (refmac 5.2.0019) with ncs restraints also 
runs fine.

Has anyone else come across this problem?

I am operating on a linux PC running Suse 10.2

Thanks very much in advance for any suggestions as to how to get around 
this.

Steve Carr 

Re: [ccp4bb] Is anomalous signal a different wavelength?

[Favre-Nicolin Vincent]

On jeudi 31 mai 2007, Murray, James W wrote:
> While we are talking about X-ray scattering, I have another question. If an
> X-ray is elastically scattered from an electron at an angle theta, its
> energy is the same is the incoming X-ray. However, the momentum is not the
> same, as it now has a component in a perpendicular direction (see fig
> below). As I don't believe that the conservation of momentum really is
> violated, what is the source of the discrepancy?

   You cannot correctly describe photon-electron interactions using classical 
mechanics. One reason is that the energy (among over properties) of the 
electron is quantified, so the photon cannot transfer an arbitrary amount of 
energy/momentum to the electron. So you'd have to consider the interaction 
between the photon and everything it is bound with (atom, lattice..)
   Incidentally, I think the classical delta(lambda) formula for Compton 
scattering is computed for a _free_ electron.

Vincent
-- 
Vincent Favre-Nicolin
Université Joseph Fourier

Re: [ccp4bb] Rfree into an existing mtz...

[Winter, G (Graeme)]

Hi James,

The easiest way I find is outside the GUI. On a command line type:

freerflag HKLIN foo.mtz HKLOUT bar.mtz
end

Then rename bar.mtz to foo.mtz, and you should find that the job is
done, with 5% of your reflections in the free set.

Cheers,

Graeme

-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
James Pauff
Sent: 31 May 2007 13:39
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Rfree into an existing mtz...

Good day all,

What is the best means of getting a freeR column into an existing mtz
file?  I've noticed the "Edit MTZ"
command bar in CCP4, but there are other options (such as conversion to
XPLOR and then back to MTZ) that seem to be able to accomplish the same
thing, although there appear to be changes in the reflection parameters
upon this conversion.

Basically, I just want to add a freeR column to monitor my
refinement(s).

Thank you as usual.


   

Looking for a deal? Find great prices on flights and hotels
with Yahoo! FareChase.
http://farechase.yahoo.com/

Re: [ccp4bb] Rfree into an existing mtz...

[Eleanor Dodson]

uniqueify this.mtz

this generates all indices to your high resln limit, adds freer and 
outputs this-unique.mtz


Is this what you want?
Eleanor

James Pauff wrote:

Good day all,

What is the best means of getting a freeR column into
an existing mtz file?  I've noticed the "Edit MTZ"
command bar in CCP4, but there are other options (such
as conversion to XPLOR and then back to MTZ) that seem
to be able to accomplish the same thing, although
there appear to be changes in the reflection
parameters upon this conversion.

Basically, I just want to add a freeR column to
monitor my refinement(s).

Thank you as usual.


   
Looking for a deal? Find great prices on flights and hotels with Yahoo! FareChase.

http://farechase.yahoo.com/


  

[ccp4bb] Rfree into an existing mtz...

[James Pauff]

Good day all,

What is the best means of getting a freeR column into
an existing mtz file?  I've noticed the "Edit MTZ"
command bar in CCP4, but there are other options (such
as conversion to XPLOR and then back to MTZ) that seem
to be able to accomplish the same thing, although
there appear to be changes in the reflection
parameters upon this conversion.

Basically, I just want to add a freeR column to
monitor my refinement(s).

Thank you as usual.


   
Looking
 for a deal? Find great prices on flights and hotels with Yahoo! FareChase.
http://farechase.yahoo.com/

Re: [ccp4bb] Is anomalous signal a different wavelength?

[Jon Wright]

James,

At least for diffraction experiments; the photon scatters off of the 
*crystal lattice*, not any individual electron, so you can conserve the 
momentum of the photons and the macroscopic crystal without the crystal 
recoiling too much.


Best,

Jon



Murray, James W wrote:


Dear All,

While we are talking about X-ray scattering, I have another question. If 
an X-ray is elastically scattered from an electron at an angle theta, 
its energy is the same is the incoming X-ray. However, the momentum is 
not the same, as it now has a component in a perpendicular direction 
(see fig below). As I don't believe that the conservation of momentum 
really is violated, what is the source of the discrepancy?


Contrast this with most textbook descriptions of Compton scattering, 
where the X-ray loses energy and the electron gains kinetic energy.


best wishes

James

X-ray > e-
 \
  \
   \


Dr. James Murray
Biochemistry Building
Department of Biological Sciences
Imperial College London
London, SW7 2AZ
Tel: +44 (0)20 7594 5276

[ccp4bb] Protein Crystallizer- AstraZeneca

[Ek, Margareta E]

Protein Crystallizer - AstraZeneca, Mölndal, Sweden

Proffice is one of the fastest growing companies within the Nordic region, 
according to Growth Plus. Proffice provides flexible staffing solutions such as 
temporary staffing, recruiting, outsourcing and career and development 
programs. Proffice operates in Denmark, Finland, Norway and Sweden. Proffice AB 
is listed on the Stockholmsbörsen (Stockholm Stock Exchange).

Proffice is now looking for a talented scientist to join the Protein 
Crystallization team for a 12 months temporary position at the Global 
Structural Chemistry Laboratory at AstraZeneca R&D Mölndal, Sweden.

The Global Structural Chemistry Laboratory, Mölndal is a centre of excellence 
supporting the AstraZeneca discovery organizations in Sweden, UK and US. 
The laboratory has around 45 scientists engaged in experimental research and 
the core disciplines are protein engineering, NMR spectroscopy and protein 
crystallography. The protein crystallography capability currently employs 6 
protein crystallizers headed by Margareta Ek and 9 crystallographers headed by 
Helena Käck. The lab is excellently equipped with state of the art equipment. 

Working within multi disciplinary teams, the candidate's main role is to enable 
structural information to assist in the process by providing well diffracting 
protein crystals that will lead to determination of the 3D structure of the 
drug target. The work includes characterization, formulation, crystallization 
and data collection, which are done in close collaboration with the other  
teams at the department.

We hope to attract a team player who is an enthusiastic, flexible individual 
with a good ability to communicate effectively.

For additional information about the position, please contact Anita Gustafsson, 
Proffice Life Science +46 31-80 76 05 or Margareta Ek  +46 31-7065243, 
AstraZeneca R&D.

To apply for the position please visit our website: www.proffice.se 
 or send your application  via mail to [EMAIL 
PROTECTED] 

Durability
12 months 

Salary
Salary according to agreement

Contact person
Anita Gustafsson, 031-807605, [EMAIL PROTECTED] 

Re: [ccp4bb] Is anomalous signal a different wavelength?

[Ian Tickle]

I think it's to do with the Uncertainty Principle.  You can't say for
sure that a particular X-ray photon has gone off in that direction (if
you could you would know both its position and momentum accurately which
is not allowed).  If you integrated the momentum over all possible
outcomes I'm sure you would find that it's conserved (it has to be in an
elastic collision).

-- Ian

> -Original Message-
> From: [EMAIL PROTECTED] 
> [mailto:[EMAIL PROTECTED] On Behalf Of Murray, James W
> Sent: 31 May 2007 10:30
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: RE: [ccp4bb] Is anomalous signal a different wavelength?
> 
> 
> Dear All,
> 
> While we are talking about X-ray scattering, I have another 
> question. If an X-ray is elastically scattered from an 
> electron at an angle theta, its energy is the same is the 
> incoming X-ray. However, the momentum is not the same, as it 
> now has a component in a perpendicular direction (see fig 
> below). As I don't believe that the conservation of momentum 
> really is violated, what is the source of the discrepancy?
> 
> Contrast this with most textbook descriptions of Compton 
> scattering, where the X-ray loses energy and the electron 
> gains kinetic energy.
> 
> best wishes
> 
> James
> 
> X-ray > e-
>  \
>   \
>\
> 
> 
> Dr. James Murray
> Biochemistry Building
> Department of Biological Sciences
> Imperial College London
> London, SW7 2AZ
> Tel: +44 (0)20 7594 5276
> 
> 
> 
> 
> 
> 


Disclaimer
This communication is confidential and may contain privileged information 
intended solely for the named addressee(s). It may not be used or disclosed 
except for the purpose for which it has been sent. If you are not the intended 
recipient you must not review, use, disclose, copy, distribute or take any 
action in reliance upon it. If you have received this communication in error, 
please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy 
all copies of the message and any attached documents. 
Astex Therapeutics Ltd monitors, controls and protects all its messaging 
traffic in compliance with its corporate email policy. The Company accepts no 
liability or responsibility for any onward transmission or use of emails and 
attachments having left the Astex Therapeutics domain.  Unless expressly 
stated, opinions in this message are those of the individual sender and not of 
Astex Therapeutics Ltd. The recipient should check this email and any 
attachments for the presence of computer viruses. Astex Therapeutics Ltd 
accepts no liability for damage caused by any virus transmitted by this email. 
E-mail is susceptible to data corruption, interception, unauthorized amendment, 
and tampering, Astex Therapeutics Ltd only send and receive e-mails on the 
basis that the Company is not liable for any such alteration or any 
consequences thereof.
Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, 
Cambridge CB4 0QA under number 3751674

Re: [ccp4bb] Is anomalous signal a different wavelength?

[Murray, James W]

Dear All, 

While we are talking about X-ray scattering, I have another question. If an 
X-ray is elastically scattered from an electron at an angle theta, its energy 
is the same is the incoming X-ray. However, the momentum is not the same, as it 
now has a component in a perpendicular direction (see fig below). As I don't 
believe that the conservation of momentum really is violated, what is the 
source of the discrepancy?

Contrast this with most textbook descriptions of Compton scattering, where the 
X-ray loses energy and the electron gains kinetic energy.

best wishes

James

X-ray > e- 
 \
  \
   \


Dr. James Murray
Biochemistry Building
Department of Biological Sciences
Imperial College London
London, SW7 2AZ
Tel: +44 (0)20 7594 5276

Re: [ccp4bb] Is anomalous signal a different wavelength?

[Marc SCHILTZ]

Ethan A Merritt wrote:

And please note that "resonant scattering" is not a standard term.
  


"Resonant Scattering" is now the standard term accepted and used 
anywhere in the X-ray physics and crystallography literature, except in 
protein crystallography.


It is the more adequate term since the X-ray phenomena under discussion 
involve resonant interactions of photons with matter and are actually 
not at all 'anomalous'.


--
Marc SCHILTZ  http://lcr.epfl.ch

Re: [ccp4bb] I vs. 2theta plot, image processing

[Jon Wright]

Fit2d is perhaps the 'gold standard' for making powder diagrams:

http://www.esrf.eu/computing/scientific/FIT2D/

See also:

http://www.datasqueezesoftware.com/

For source code try:

http://cctbx.sourceforge.net/current_cvs/python/iotbx.detectors.html

Good luck,

Jon



-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Lucas Bleicher
Sent: 30 May 2007 17:58
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] I vs. 2theta plot, image processing

1) Some data collection and image processing files have the options to show the intensity 
distribution over a user-defined "line" in the image. Does any program allow 
one to trace a line from the beam center to the detector edge and save this intensity 
distribution to a file, so one could have I vs. 2theta data (or even a I vs. pixel data 
file, which could be easily converted to a I vs. 2theta file given the experimental 
setup)?

2) Is there a program which could convert image files from common 2D detectors 
(Mar345, MarCCD, RaxisII...) to a text file with the intensity on each pixel so 
one could easily write programs to do things such as in (1)?

3) If the answer to 2 is "No, you should learn how to handle binary files and image 
data formats", is there a tutorial on how to do this (I would prefer C/C++, but 
Fortran is OK), or some well-documented open source code I could study?

Thanks,
Lucas Bleicher

__
Fale com seus amigos  de graça com o novo Yahoo! Messenger http://br.messenger.yahoo.com/ 

Re: [ccp4bb] I vs. 2theta plot, image processing

[Winter, G (Graeme)]

Hi Lucas,

There is a C++ library called DiffractionImage which may help with #3 if you 
get that far:

http://www.ccp4.ac.uk/newsletters/newsletter45/articles/DiffractionImage.html

If you get in touch with Francois Remacle I'm sure he'll send you everything 
you need.

Cheers,

Graeme 

-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Lucas Bleicher
Sent: 30 May 2007 17:58
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] I vs. 2theta plot, image processing

1) Some data collection and image processing files have the options to show the 
intensity distribution over a user-defined "line" in the image. Does any 
program allow one to trace a line from the beam center to the detector edge and 
save this intensity distribution to a file, so one could have I vs. 2theta data 
(or even a I vs. pixel data file, which could be easily converted to a I vs. 
2theta file given the experimental setup)?

2) Is there a program which could convert image files from common 2D detectors 
(Mar345, MarCCD, RaxisII...) to a text file with the intensity on each pixel so 
one could easily write programs to do things such as in (1)?

3) If the answer to 2 is "No, you should learn how to handle binary files and 
image data formats", is there a tutorial on how to do this (I would prefer 
C/C++, but Fortran is OK), or some well-documented open source code I could 
study?

Thanks,
Lucas Bleicher

__
Fale com seus amigos  de graça com o novo Yahoo! Messenger 
http://br.messenger.yahoo.com/ 

Re: [ccp4bb] Is anomalous signal a different wavelength?

[Marius Schmidt]

Especially, the crystallographers are interested
in everything concerning resonance scattering, which is
indeed a valid terminus technicus in natural sciences.
The question of Jacob is very interesting. We have to
distinguish between absorption cross section and 
scattering cross section and relate them, say, by
Kramers Kronig. 
As I see it: The total scattering cross section of
an electron depends on the eigenfrequency and the
constant of friction of the electron bound to the
nucleus. Near resonance the total scattering cross
section increases dramatically and the proability
to scatter an X-ray is much larger than remote from
the edge. However, this scattering process is elastic:
it means that the wavelength is NOT altered. However,
a phase shift of the scattered photon occurs which is
different from the 180 deg usually expected for Thompson
scattering. We have to correct for this (Hönl-correction)
and this gives us also the opportunity to determine phase.

If really absorption occurs, of course we have fluorescence
which has lost all the phase relation relative to the
incident photon and is indeed not scattered in reflections
anymore, EXCEPT when there are collective processes as 
for example observed in "nuclear resonance scattering" 
of Mössbauer radiation.

Marius

> Dear Crystallographers,
> 
> I have been wondering recently whether the anomalous component of a
> diffraction pattern is of a
> different wavelength from the regular diffraction pattern. It seems
> reasonable as resonant
> scattering seems to be akin to fluorescence, although as I understand
> it, is not exactly the same.
> Does anybody know here for sure, or at least where to look or whom to
> ask?
> 
> All the best,
> 
> Jacob Keller
> 
> ***
> Jacob Keller
> Northwestern University
> 6541 N. Francisco #3
> Chicago IL 60645
> (847)467-4049
> [EMAIL PROTECTED]
> ***

PD Dr. habil. Marius Schmidt
Physikdepartment E17
Technische Universitaet Muenchen
James Franck Strasse
85747 Garching/Germany
email: [EMAIL PROTECTED]
http://users.physik.tu-muenchen.de/marius/
phone: +49-(0)89-2891-2550
fax:   +49-(0)89-2891-2548