[ccp4bb] install Arp/warp failed in CCP4i

[deliang]

Hi CCP4ers,

Need your help, many thanks.

When I was trying to install arp_warp_7.0.1.tar.gz in my CCP4i (6.0.windows 
version), it complained as " Failed to unpack and/or read contents of 
C:/CcprTemp/arp_warp_7.0.1.tar.gz. This may not be a valid CCP4i package.

Then, I unzipped this file, and found out a file named:ARP_wARP_CCP4I6.tar.gz.  
Therefore, I instructed CCP4i to install this file, and it works! CCP4i said: 
Installation of "ARP_wARP_CCP4I6" completed successfully. Restart CCP4i to see 
the new tasks in the menu."

Everything sounds ok. I restarted pc, ccp4i, and tried to lauch Arp/warp. Then 
it complained again: Can not get environment variable for warpdoc! 
followed by
bad window path name ".warning.main.canvas.contents.protocol"

bad window path name ".warning.main.canvas.contents.protocol"

while executing

"frame $line"

(procedure "CreateLine" line 38)

invoked from within

"CreateLine line  message "Enter job title (use only alphanumeric, spaces, 
brackets and underscores)"  help  title  label "Job title"  widget $element ..."

(procedure "CreateTitleLine" line 12)

invoked from within

"CreateTitleLine line TITLE"

(procedure "arp_warp_task_window" line 17)

invoked from within

"arp_warp_task_window arp_warp"

("eval" body line 1)

invoked from within

"eval "$cmd""

(procedure "RunTask" line 109)

invoked from within

"RunTask arp_warp"

invoked from within

".module.menu.action.canvas.frame.t.f_5 invoke"

("uplevel" body line 1)

invoked from within

"uplevel #0 [list $w invoke]"

(procedure "tk::ButtonUp" line 24)

invoked from within

"tk::ButtonUp .module.menu.action.canvas.frame.t.f_5"

(command bound to event)

[ccp4bb] auto-superpositions script, pymol or otherwise

[Jacob Keller]

Dear Crystallographers,

Quasi-off-topic question:

does anybody have a script to download and superimpose automatically some set 
of similar structures in the PDB, perhaps as defined by DALI? Preferably this 
would be for pymol...

Jacob


***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.491.2438
cel: 773.608.9185
email: j-kell...@northwestern.edu
***

  - Original Message - 
  From: mjvdwo...@netscape.net 
  To: CCP4BB@JISCMAIL.AC.UK 
  Sent: Monday, January 12, 2009 7:14 PM
  Subject: Re: [ccp4bb] structure (factor) amplitude


  But Tassos, you and Gerard both should know better (Mark vR already knows, 
clearly). THAT is not Dutch diplomacy, because it always starts like this:

  No, no, no, you are completely wrong!

  Actually, the way I learned about Cicero is better explained with Gaius 
Julius Ceasar. There is a temporal difference in pronunciation. The "early 
schools" (such as Leiden Univ.) teach [ˈsiːzɚ] while "later schools" (such as 
Nijmegen Univ.) teach [ˈkaɪsar]. Early and late are of course defined on the 
Roman time scale and it is theoretically possible, after 30 years, that I have 
my time scale running in the wrong direction, but that would be too diplomatic 
to add and I don't think so: "classical" is defined as roughly 100BC to 100AD 
and the more modern [ˈkaɪsar] even tually "stuck". It is of course obvious that 
the latter has lead to the German Kaiser and Dutch keizer. 

  So if you can have two kinds of Ciceros and two kinds of Ceasars, and we all 
understand what they are, you can also have Structure (Factor) Amplitude both 
ways and still understand? 

  Personally I would always leave "Factor" in there. Somehow in my simplistic 
mind "F" comes from Factor. So to BR: please do keep the Factor. Perhaps you 
will aid consensus by creating more Factor hits in google in the future.

  Mark

  (Who now wonders, Nomen est Omen?)




  -Original Message-
  From: Anastassis Perrakis 
  To: CCP4BB@JISCMAIL.AC.UK
  Sent: Mon, 12 Jan 2009 7:15 am
  Subject: Re: [ccp4bb] structure (factor) amplitude


  This chain reminds me of another discussion we had during dinner at Grenoble 
in the late '90s. 
  The topic of the argument was how to pronounce the name 'Cicero'. 
  Namely, my Italian friend (Gino C) was claiming it should be pronounced like 
in modern Italian, 'Chichero', 
  while I was claiming that since the contemporary Greeks20transcribed it as 
'Kikero' (with a k) 
  it should indeed sound as in modern Greek, Kikero. 
   
  My learned Dutch colleague (Mark vR) after a few minutes of this rather dull 
argument he exclaimed in the well known 
  Dutch diplomatic manner: 'But, who chares?' 
   
  Not that I don't care, but I would personally understand the same thing in 
both cases - and I am enjoying the argument. 
   
A. 
   
  PS Wikipedia says: Marcus Tullius Cicero (Classical Latin pronounced 
[ˈkikeroː], usually pronounced /ˈsɪsəɹəʊ/ in English; January 3, 106 BC – 
December 7, 43 BC) was a Roman statesman, lawyer, political theorist, 
philosopher, and Roman constitutionalist. 
   
  On Jan 12, 2009, at 14:48, Ian Tickle wrote: 
   
  > Hi Gerard & Marc 
  > 
  > My answer was my interpretation of Bernhard's original question "what 
  > *is* the currently accepted name of the object whose description is 
  > 'structure factor amplitude' ?", and was based both on authoritative 
  > precedent, i.e. ITC Vol. B, and on frequency of current usage, i.e. 
  > Google hits. Carroll was making the point that in logic the name of > an 
  > object is minimally only an arbitrary string of characters (preferably 
  > pronounceable!), like the name of a variable in a program, which 
  > minimally need have no semantic connotations whatsoever: "a rose by > any 
  > other name would smell as sweet". The only requirement is that it > must 
  > not be ambiguous, i.e. you can't have two different objects within the 
  > same context with the same name. For example my name 'Ian' provides > no 
  > semantic clues as to my description (except perhaps that I'm male), > and 
  > causes no problems provided no other 'Ian's enter the discussion. 
  > However alternate names for the same object are clearly allowed 
  > (consider names of objects in different languages). 
  > 
  > In this case I am not offering an opinion on what I think the name 
  > *should be*, I am merely reporting on what the name *is* (however 
  > illogical), based on precedent and usage. However I do accept your 
  > argument that when making up the compound name of an object, it should 
  > as far as possible also be accurately descriptive in the way it > relates 
  > to the names of related objects, consistent with the conflicting needs 
  > for abbreviation and lack of ambiguity. You are going much further > than 
  > m

Re: [ccp4bb] structure (factor) amplitude

[mjvdwoerd]

 But Tassos, you and Gerard both should know better (Mark vR already knows, 
clearly). THAT is not Dutch diplomacy, because it always starts like this:

No, no, no, you are completely wrong!

Actually, the way I learned about Cicero is better explained with Gaius Julius 
Ceasar. There is a temporal difference in pronunciation. The "early schools" 
(such as Leiden Univ.) teach [ˈsiːzɚ]
while "later schools" (such as Nijmegen Univ.) teach [ˈkaɪsar]. Early and late 
are of course defined on the Roman time scale and it is theoretically possible, 
after 30 years, that I have my time scale running in the wrong direction, but 
that would be too diplomatic to add and I don't think so: "classical" is 
defined as roughly 100BC to 100AD and the more modern [ˈkaɪsar] eventually 
"stuck". It is of course obvious that the latter has lead to the German Kaiser 
and Dutch keizer. 

So if you can have two kinds of Ciceros and two kinds of Ceasars, and we all 
understand what they are, you can also have Structure (Factor) Amplitude both 
ways and still understand? 

Personally I would always leave "Factor" in there. Somehow in my simplistic 
mind "F" comes from Factor. So to BR: please do keep the Factor. Perhaps you 
will aid consensus by creating more Factor hits in google in the future.

Mark

(Who now wonders, Nomen est Omen?)




 

-Original Message-
From: Anastassis Perrakis 
To: CCP4BB@JISCMAIL.AC.UK
Sent: Mon, 12 Jan 2009 7:15 am
Subject: Re: [ccp4bb] structu
re (factor) amplitude









This chain reminds me of another discussion we had during dinner at Grenoble in 
the late '90s. 

The topic of the argument was how to pronounce the name 'Cicero'. 

Namely, my Italian friend (Gino C) was claiming it should be pronounced like in 
modern Italian, 'Chichero', 

while I was claiming that since the contemporary Greeks transcribed it as 
'Kikero' (with a k) 

it should indeed sound as in modern Greek, Kikero. 
 

My learned Dutch colleague (Mark vR) after a few minutes of this rather dull 
argument he exclaimed in the well known 

Dutch diplomatic manner: 'But, who chares?' 
 

Not that I don't care, but I would personally understand the same thing in both 
cases - and I am enjoying the argument. 
 

   A. 
 

PS Wikipedia says: Marcus Tullius Cicero (Classical Latin pronounced 
[ˈkikeroː], usually pronounced /ˈsɪsəɹəʊ/ in English; January 3, 106 BC – 
December 7, 43 BC) was a Roman statesman, lawyer, political theorist, 
philosopher, and Roman constitutionalist. 
 

On Jan 12, 2009, at 14:48, Ian Tickle wrote: 
 

> Hi Gerard & Marc 

> 

> My answer was my interpretation of Bernhard's original question "what 

> *is* the currently accepted name of the object whose description is 

> 'structure factor amplitude' ?", and was based both on authoritative 

> precedent, i.e. ITC Vol. B, and on frequency of current usage, i
.e. 

> Google hits.  Carroll was making the point that in logic the name of > an 

> object is minimally only an arbitrary string of characters (preferably 

> pronounceable!), like the name of a variable in a program, which 

> minimally need have no semantic connotations whatsoever: "a rose by > any 

> other name would smell as sweet".  The only requirement is that it > must 

> not be ambiguous, i.e. you can't have two different objects within the 

> same context with the same name.  For example my name 'Ian' provides > no 

> semantic clues as to my description (except perhaps that I'm male), > and 

> causes no problems provided no other 'Ian's enter the discussion. 

> However alternate names for the same object are clearly allowed 

> (consider names of objects in different languages). 

> 

> In this case I am not offering an opinion on what I think the name 

> *should be*, I am merely reporting on what the name *is* (however 

> illogical), based on precedent and usage.  However I do accept your 

> argument that when making up the compound name of an object, it should 

> as far as possible also be accurately descriptive in the way it > relates 

> to the names of related objects, consistent with the conflicting needs 

> for abbreviation and lack of ambiguity.  You are going much further > than 

> me: you are answering a different question "what *should be* the=C
2

> accepted name of ... ?".  In this case you have clearly made a strong 

> argument, which I accept, for establishing an alternate name for this 

> particular object.  However one should not create new names or change 

> the names of objects lightly, if misunderstandings are to be avoided. 

> Fortunately in this case it can be done with minimal > misunderstanding on 

> the part of the readers of Bernhard's textbook (though others may 

> disagree on that point), provided it is pointed out that there is 

> precedent for an alternative name for the object in question, and 

> perhaps a reference should be made to the original authoritative 

> definition. 

> 

> Cheers 

> 

> -- Ian 

> 

>> -Original Messa

Re: [ccp4bb] Ligand binding in multiple conformation

[Bernhard Rupp]

Quite precise occupancy.

-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Aaron
Oakley
Sent: Monday, January 12, 2009 4:19 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Ligand binding in multiple conformation

 

>I had a question about flexibility in ligand binding in an enzyme active
site.
>Is it possible for a substrate/product analogue to bind in more than one
conformation in the active site.

Yes. It is even possible for portions of a ligand to be disordered and not
discernable in electron density.

>Since the ligand/enzyme interactions are very specific I am a little
confused about this.
>Also which program would you use if you have to refine with alternate
ligand conformation.

REFMAC will do this just fine. Just make sure you have the "A", "B"
conformers set in the PDB file.

EG:

ATOM 72  CA APRO A   7  -2.619  28.983  -0.796  0.62  6.48
C  
ATOM 73  CA BPRO A   7  -2.226  29.044  -0.847  0.38  5.76
C  

Re: [ccp4bb] Ligand binding in multiple conformation

[Aaron Oakley]

 

>I had a question about flexibility in ligand binding in an enzyme active site.
>Is it possible for a substrate/product analogue to bind in more than one 
>conformation in the active site.

Yes. It is even possible for portions of a ligand to be disordered and not 
discernable in electron density.

>Since the ligand/enzyme interactions are very specific I am a little confused 
>about this.
>Also which program would you use if you have to refine with alternate ligand 
>conformation.

REFMAC will do this just fine. Just make sure you have the "A", "B" conformers 
set in the PDB file.

EG:

ATOM 72  CA APRO A   7  -2.619  28.983  -0.796  0.62  6.48   C  
ATOM 73  CA BPRO A   7  -2.226  29.044  -0.847  0.38  5.76   C  

Re: [ccp4bb] Ligand binding in multiple conformation

[Chandra Verma]

hi

yes this may happen in some circumstanceshave a look at

J Am Chem Soc. 2008 Oct 15;130(41):13514-5.


> Hi,
>
> I had a question about flexibility in ligand binding in an enzyme active
> site.  Is it possible for a substrate/product analogue to bind in more
> than
> one conformation in the active site.  Since the ligand/enzyme interactions
> are very specific I am a little confused about this.
> Also which program would you use if you have to refine with alternate
> ligand
> conformation.
> Please mention if you have ever come across any paper that explains such a
> phenomena.
> Thanks a lot.
>
> Mariah
> --
> Mariah Jones
> Department of Biochemistry
> University of Florida
>

Re: [ccp4bb] Ligand binding in multiple conformation

[Kendall Nettles]

Hi Mariah, 
We have had one case of this, with two partially overlapping conformations
of a ligand, which is not yet published.

Model in both ligand  conformations. Then edit the PDB to give them the same
Chain ID, but with alternative conformations for each atom, or each one that
is different. You might try giving 0.5 occupancy to each for REFMAC
refinement. In Phenix you can also refine the occupancy. Here is an example
for the CAA atom of our drug.

ATOM  7090  CAAADRG E  1   9.312   2.643   8.223 0.50 42.57   C
ATOM  7091  CAABDRG E  1 12.707   2.133  -0.186  0.50 36.22  C

Regards, 
Kendall

-- 
Kendall W. Nettles, PhD
Asssociate Professor
Department of Cancer Biology
The Scripps Research Institute
5353 Parkside Dr.
Jupiter Fl 33458





On 1/12/09 6:52 PM, "protein.chemist protein.chemist" 
wrote:

> 
> Hi,
> 
> I had a question about flexibility in ligand binding in an enzyme active site.
> Is it possible for a substrate/product analogue to bind in more than one
> conformation in the active site.  Since the ligand/enzyme interactions are
> very specific I am a little confused about this.
> Also which program would you use if you have to refine with alternate ligand
> conformation.
> Please mention if you have ever come across any paper that explains such a
> phenomena.
> Thanks a lot.
> 
> Mariah

[ccp4bb] Ligand binding in multiple conformation

[protein.chemist protein.chemist]

Hi,

I had a question about flexibility in ligand binding in an enzyme active
site.  Is it possible for a substrate/product analogue to bind in more than
one conformation in the active site.  Since the ligand/enzyme interactions
are very specific I am a little confused about this.
Also which program would you use if you have to refine with alternate ligand
conformation.
Please mention if you have ever come across any paper that explains such a
phenomena.
Thanks a lot.

Mariah
-- 
Mariah Jones
Department of Biochemistry
University of Florida

Re: [ccp4bb] structure (factor) amplitude

[Ian Tickle]

 

> -Original Message-
> From: marc.schi...@epfl.ch [mailto:marc.schi...@epfl.ch] 
> Sent: 12 January 2009 22:35
> To: Ian Tickle
> Cc: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] structure (factor) amplitude
> 
> Ian Tickle wrote:
> 
> OK, limiting the vote to people whom I think we can assume know what
> vaguely they're talking about, i.e. Acta Cryst. / J. Appl. Cryst.
> authors, and using the IUCr search engine we get 553 hits for 
> "structure
> amplitude" and 256 for "structure factor amplitude"
> 
> But be warned that not all Acta Cryst. authors give the term  
> "structure amplitude"  the meaning that you think they do, i.e. a  
> shortcut version for "structure factor amplitude" !

Actually it seems that "structure amplitude" in the |F| sense was
historically derived as a shortcut version of "magnitude of the
structure amplitude factor", not of "structure factor amplitude" which
is obviously derived directly from "structure factor".  Similarly
"structure factor" was derived as a shortcut version of "structure
amplitude factor", but it has now unfortunately acquired at least 2
entirely different meanings as you point out.

The term "structure amplitude" clearly goes back a long way, it's much
older than "structure factor amplitude", and originally meant something
else entirely, as Gerard pointed out, so again we have ambiguous
terminology!

"Structure factor amplitude" (or maybe "modulus" or "magnitude" would
be better to avoid the historical ambiguities surrounding the term
"amplitude") has the clear advantage that it is relatively recent
terminology and hasn't had time yet to acquire ambiguous meanings, so I
would vote for it on that count alone!

Cheers

-- Ian


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Re: [ccp4bb] structure (factor) amplitude

[Jacob Keller]

- Original Message - 
From: "Bernhard Rupp" 

To: 
Sent: Saturday, January 10, 2009 4:09 PM
Subject: [ccp4bb] structure (factor) amplitude



Dear All,

I am getting conflicting comments on the use of
'structure factor amplitude'
vs. just
'structure amplitude'
for |F|.

Is there some 'modern' consensus on a preference?

Best, BR




From the course of this thread, the answer to your actual original question 
appears to be a resounding "no!" And further, there seems not even to be a 
consensus in non-modern circles!


JPK

Re: [ccp4bb] structure (factor) amplitude

[marc . schiltz]

Ian Tickle wrote:

OK, limiting the vote to people whom I think we can assume know what
vaguely they're talking about, i.e. Acta Cryst. / J. Appl. Cryst.
authors, and using the IUCr search engine we get 553 hits for "structure
amplitude" and 256 for "structure factor amplitude"




But be warned that not all Acta Cryst. authors give the term  
"structure amplitude"  the meaning that you think they do, i.e. a  
shortcut version for "structure factor amplitude" !


In particular, P.P. Ewald (no less an authority than the ones you  
quote), uses the term "structure amplitude" for the complex number  
F(hkl). See e.g. Acta Cryst. A35 (1979), page 8.


To my surprise, M. von Laue in his treatise  
"Rontgenstrahlinterferenzen" also uses the term structure amplitude  
("Strukturamplitude") for the complex quantity F. He defines the  
structure factor ("Strukturfaktor") as the square-modulus of F. This  
seems to go back to early papers by P.P. Ewald. Both of these  
quantities are also defined in exactly the same way by Hosemann &  
Bagchi in their 1962 textbook on X-ray diffraction. In optics it makes  
perfect sense to speak about complex amplitudes.


We thus have the "historic" definitions :

"structure amplitude" = complex F

"structure factor" = square-modulus of F

This comes from the fact that the intensity formulae which these  
authors derive, and which remain valid for finite crystals and for  
paracrystals, there is a neat factorization into a lattice-factor  
("Gitterfaktor") on one hand and a structure factor ("Strukturfaktor")  
on the other hand. The lattice factor only depends on the number and  
spatial arrangement of unit cells within the crystal, whereas the  
structure factor only depends on the atomic structure of one unit  
cell. The latter is of course equal to the square-modulus of F.


To add to the confusion: Current-day small-angle scattering (SAXS)  
specialists call "structure factor" the quantity which von Laue would  
have called "lattice factor" (and they call "formfactor" the quantity  
which von Laue called "structure factor") .


Seems that there will be little agreement

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


Ian Tickle wrote:

OK, limiting the vote to people whom I think we can assume know what
vaguely they're talking about, i.e. Acta Cryst. / J. Appl. Cryst.
authors, and using the IUCr search engine we get 553 hits for "structure
amplitude" and 256 for "structure factor amplitude"


But be warned that not all Acta Cryst. authors give the term "structure 
amplitude"  the meaning that you think they do, i.e. a shortcut version for 
"structure factor amplitude" !

In particular, P.P. Ewald (no less an authority than the ones you quote), uses 
the term "structure amplitude" for the complex number F(hkl). See e.g. Acta 
Cryst. A35 (1979), page 8.

To my surprise, M. von Laue in his treatise "Rontgenstrahlinterferenzen" also 
uses the term structure amplitude ("Strukturamplitude") for the complex 
quantity F. He defines the structure factor ("Strukturfaktor") as the 
square-modulus of F. This seems to go back to early papers by P.P. Ewald. Both 
of these quantities are also defined in exactly the same way by Hosemann & 
Bagchi in their 1962 textbook on X-ray diffraction. In optics it makes perfect 
sense to speak about complex amplitudes.

We thus have the "historic" definitions :

"structure amplitude" = complex F

"structure factor" = square-modulus of F

This comes from the fact that the intensity formulae which these authors 
derive, and which remain valid for finite crystals and for paracrystals, there 
is a neat factorization into a lattice-factor ("Gitterfaktor") on one hand and 
a structure factor ("Strukturfaktor") on the other hand. The lattice factor 
only depends on the number and spatial arrangement of unit cells within the 
crystal, whereas the structure factor only depends on the atomic structure of 
one unit cell. The latter is of course equal to the square-modulus of F.

To add to the confusion: Current-day small-angle scattering (SAXS) specialists 
call "structure factor" the quantity which von Laue would have called "lattice 
factor" (and they call "formfactor" the quantity which von Laue called 
"structure factor") .

Seems that there will be little agreement

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

Ian Tickle wrote:

OK, limiting the vote to people whom I think we can assume know what
vaguely they're talking about, i.e. Acta Cryst. / J. Appl. Cryst.
authors, and using the IUCr search engine we get 553 hits for "structure
amplitude" and 256 for "structure factor amplitude"


Well, then you may be warned that not all Acta Cryst. authors give the term 
"structure amplitude"  the meaning that you think they do, i.e. a shortcut 
version of "structure factor amplitude" !

In particular, P.P. Ewald (no less an authority than the ones you quote), uses 
the term structure amplitude for the complex number F(hkl). See Acta Cryst. A35 
(1979), page 8.

Re: [ccp4bb] structure (factor) amplitude

[James Stroud]

On Jan 12, 2009, at 11:09 AM, Ethan Merritt wrote:

"geometrical structure factor" gets 68 hits in the IUCr search engine,
and 2190 GHits   (GHits == Google Hits)


To avoid confusion, can we use "gHit" as a google Hit unit? First,  
"google" is traditionally spelled with a lowercase "g"[1]. Second, one  
can appreciate the practicality of this form when writing 10**9 Hits  
(G gHit), especially considering the natural tendency to drop the  
leading g when the context is understood (e.g. G Hit).


James

[1] www.google.com

Re: [ccp4bb] 2D

[Puey Ounjai]

Dear,
So what is the problem? to be honest with you, I have hardly heard that
someone use hanging drop vapour diffusion to glow 2D crystal because usually
you ll end up have 3D crystal or severe stacking problem.

I guess one of your major problem might be stacking, If this is the
case, you should try to use lipid monolayer technique. You can check
original streptavidin paper by Darst SA and Kornberg RD. In this technique,
it relies mostly on how homogeneous your protein  is (which I believe you
already have it) and the sufficiently good binding of the protein on the
surface of the lipid monolayer which you have to figure out (either using
electrostatic interaction or employing different tags).

One good thing about his technique is that if you want to solve structure of
this protein using electron crystallography, then you ll never have problem
with figure out how to make it to stick to your grid which is one of the
major problem many 2D people have encountered including me :P.

Hope that helps,
Puey


On Mon, Jan 12, 2009 at 10:24 AM,  wrote:

> Hi,
> Thanks for the suggestion. Here is more info: It is a soluble protein, a
> monomer has 3alpha and 3 beta subunits, and exists in solution as a dimer.
> The technique is hanging drop, vapor diffusion.  And the  mother liquor is
> ~ 0.1 mM cacodylate pH 6.2ish, MgCl2 and PEG 20k.
>
> =v=
>
>
> -Original Message-
> From: Puey Ounjai 
> To: CCP4BB@JISCMAIL.AC.UK
> Sent: Fri, 9 Jan 2009 3:56 pm
> Subject: Re: [ccp4bb] 2D
>
> Hello,
>
> The information you provided to us here is not enough. there are so many
>
> parameters and
>
> so many means to optimize 2D crystal. All of which depends on what kind of
>
> protein you
>
> are working on (membrane associated or soluble) and what kind of technique 
> that
>
> you use
>
> to grow your crystal (lipid monolayer, dialysis or else).
>
>
> I guess unless you give us more info about your crystal otherwise it will be
>
> quite difficult
>
> for us to help you optimize your condition.
>
>
> Sincerely,
>
> Puey
>
>
> --
> *A Good Credit Score is 700 or Above. See yours in just 2 easy 
> steps!
> *
>

Re: [ccp4bb] structure (factor) amplitude

[Jacob Keller]

My apologies as well about the incomplete James perusal. I was just looking 
for either term in the table of contents, and assumed that a similar meaning 
would apply to such a similar (identical) term. Perhaps there are some 
structures in the PDB, then, that have Jamesian structure amplitudes?


JPK

***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.491.2438
cel: 773.608.9185
email: j-kell...@northwestern.edu
***

- Original Message - 
From: "Fischmann, Thierry" 

To: 
Sent: Monday, January 12, 2009 1:45 PM
Subject: Re: [ccp4bb] structure (factor) amplitude


I'll add my 2 calories then. Gerard's new naming carefully avoids the
"Factor" and "Amplitude". The following term should get everybody to
agree:
"FA-free STRUDL".

Example of politically correct use:
"It is good practice to deposit your FA-free STRUDL in the Protein Data
Bank along with the atomic coordinates"

Thierry

-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Gerard Bricogne
Sent: Monday, January 12, 2009 02:34 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] structure (factor) amplitude

Dear Gerard,

As usual, your contribution is a hard act to follow. However, given
that your actual proposal can be rather indigestible (especially with
lots
of cream) we might have to stick with the current options.

 What the perusal of James has revealed is that, if we want to
respect
the terminology that Ewald and he introduced, "structure amplitude" and
"structure factor amplitude" cannot be considered as synonyms - which
finally answers Bernhard's question, Google results notwithstanding.


With best wishes

 Gerard.

--
On Mon, Jan 12, 2009 at 08:21:40PM +0100, Gerard DVD Kleywegt wrote:

As suggested by Tassos, what we need now more than ever is some Dutch
diplomacy so that he healing can really begin. Various people have

argued

for a shorter term (Brazilians, Pflugrath) and since I'm personally

rather

partial to Brazilians I would say we ought to go with that and shave

off a

few letters.

So: we need a shorter, unambiguous term. I also think it should sound
delicious. And it should be related to "structure (factor)" and
"amplitude". We could take the first few letters of "STRucture", add

some

of the last ones of "amplitUDe". And to sweeten the deal (and

reflecting

the Austrian roots of Bernhard R and the Teutonic dittos of Jim P), we



could add a diminutive "l". Thus we obtain:

 STRUDL

So can we agree that, from now on, |F| is refered to as "strudl"?

Examples

of usage:

- "I have deposited my experimental strudls and sigmas, boss!"

- "We calculated a SIGMAA-weighted map with coefficients

two-m-strudl-obs

minus D-strudl-calc."

N.B.: In the special case that the |F| are the result of AP
(auto-processing) of FEL (free-electron laser) data, the appropriate

term

would obviously be: "APFELSTRUDL".

--DVD

**
   Gerard J.  Kleywegt
   Dept. of Cell & Molecular Biology  University of Uppsala
   Biomedical Centre  Box 596
   SE-751 24 Uppsala  SWEDEN

http://xray.bmc.uu.se/gerard/  mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**



--

===
* *
* Gerard Bricogne g...@globalphasing.com  *
* *
* Global Phasing Ltd. *
* Sheraton House, Castle Park Tel: +44-(0)1223-353033 *
* Cambridge CB3 0AX, UK   Fax: +44-(0)1223-366889 *
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This message and any attachments are solely for the
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disclosure, copying, use or distribution of the information
included in this message is prohibited -- Please
immediately and permanently delete.

Re: [ccp4bb] structure (factor) amplitude

[Fischmann, Thierry]

I'll add my 2 calories then. Gerard's new naming carefully avoids the
"Factor" and "Amplitude". The following term should get everybody to
agree:
"FA-free STRUDL".

Example of politically correct use:
"It is good practice to deposit your FA-free STRUDL in the Protein Data
Bank along with the atomic coordinates"

Thierry

-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Gerard Bricogne
Sent: Monday, January 12, 2009 02:34 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] structure (factor) amplitude

Dear Gerard,

 As usual, your contribution is a hard act to follow. However, given
that your actual proposal can be rather indigestible (especially with
lots
of cream) we might have to stick with the current options. 

  What the perusal of James has revealed is that, if we want to
respect
the terminology that Ewald and he introduced, "structure amplitude" and
"structure factor amplitude" cannot be considered as synonyms - which
finally answers Bernhard's question, Google results notwithstanding.


 With best wishes
 
  Gerard.

--
On Mon, Jan 12, 2009 at 08:21:40PM +0100, Gerard DVD Kleywegt wrote:
> As suggested by Tassos, what we need now more than ever is some Dutch 
> diplomacy so that he healing can really begin. Various people have
argued 
> for a shorter term (Brazilians, Pflugrath) and since I'm personally
rather 
> partial to Brazilians I would say we ought to go with that and shave
off a 
> few letters.
>
> So: we need a shorter, unambiguous term. I also think it should sound 
> delicious. And it should be related to "structure (factor)" and 
> "amplitude". We could take the first few letters of "STRucture", add
some 
> of the last ones of "amplitUDe". And to sweeten the deal (and
reflecting 
> the Austrian roots of Bernhard R and the Teutonic dittos of Jim P), we

> could add a diminutive "l". Thus we obtain:
>
>  STRUDL
>
> So can we agree that, from now on, |F| is refered to as "strudl"?
Examples 
> of usage:
>
> - "I have deposited my experimental strudls and sigmas, boss!"
>
> - "We calculated a SIGMAA-weighted map with coefficients
two-m-strudl-obs 
> minus D-strudl-calc."
>
> N.B.: In the special case that the |F| are the result of AP 
> (auto-processing) of FEL (free-electron laser) data, the appropriate
term 
> would obviously be: "APFELSTRUDL".
>
> --DVD
>
> **
>Gerard J.  Kleywegt
>Dept. of Cell & Molecular Biology  University of Uppsala
>Biomedical Centre  Box 596
>SE-751 24 Uppsala  SWEDEN
>
> http://xray.bmc.uu.se/gerard/  mailto:ger...@xray.bmc.uu.se
> **
>The opinions in this message are fictional.  Any similarity
>to actual opinions, living or dead, is purely coincidental.
> **
>

-- 

 ===
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 * Gerard Bricogne g...@globalphasing.com  *
 * *
 * Global Phasing Ltd. *
 * Sheraton House, Castle Park Tel: +44-(0)1223-353033 *
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This message and any attachments are solely for the
intended recipient. If you are not the intended recipient,
disclosure, copying, use or distribution of the information 
included in this message is prohibited -- Please 
immediately and permanently delete.

Re: [ccp4bb] structure (factor) amplitude

[Pete Meyer]

> PS: I vote for that "structure factor amplitude" be used in text books
> and |F| on cell phones.  Student of 2015: "You mean 'abs-F' is really
> pronounced 'structure factor amplitude'?  I didn't know that!"

By 2015, it would probably be some less-comprehensible variant of
instant-messenging contractions and lolcat speak, more like "U mn
'abs-F' z rl'y s'd 'structure factor amplitude'?"

I'd also vote for "structure factor amplitude", but if we're going by
PDB/RCSB usage it appears to be just "structure factor".

Re: [ccp4bb] structure (factor) amplitude

[Gerard Bricogne]

Dear Gerard,

 As usual, your contribution is a hard act to follow. However, given
that your actual proposal can be rather indigestible (especially with lots
of cream) we might have to stick with the current options. 

  What the perusal of James has revealed is that, if we want to respect
the terminology that Ewald and he introduced, "structure amplitude" and
"structure factor amplitude" cannot be considered as synonyms - which
finally answers Bernhard's question, Google results notwithstanding.


 With best wishes
 
  Gerard.

--
On Mon, Jan 12, 2009 at 08:21:40PM +0100, Gerard DVD Kleywegt wrote:
> As suggested by Tassos, what we need now more than ever is some Dutch 
> diplomacy so that he healing can really begin. Various people have argued 
> for a shorter term (Brazilians, Pflugrath) and since I'm personally rather 
> partial to Brazilians I would say we ought to go with that and shave off a 
> few letters.
>
> So: we need a shorter, unambiguous term. I also think it should sound 
> delicious. And it should be related to "structure (factor)" and 
> "amplitude". We could take the first few letters of "STRucture", add some 
> of the last ones of "amplitUDe". And to sweeten the deal (and reflecting 
> the Austrian roots of Bernhard R and the Teutonic dittos of Jim P), we 
> could add a diminutive "l". Thus we obtain:
>
>  STRUDL
>
> So can we agree that, from now on, |F| is refered to as "strudl"? Examples 
> of usage:
>
> - "I have deposited my experimental strudls and sigmas, boss!"
>
> - "We calculated a SIGMAA-weighted map with coefficients two-m-strudl-obs 
> minus D-strudl-calc."
>
> N.B.: In the special case that the |F| are the result of AP 
> (auto-processing) of FEL (free-electron laser) data, the appropriate term 
> would obviously be: "APFELSTRUDL".
>
> --DVD
>
> **
>Gerard J.  Kleywegt
>Dept. of Cell & Molecular Biology  University of Uppsala
>Biomedical Centre  Box 596
>SE-751 24 Uppsala  SWEDEN
>
> http://xray.bmc.uu.se/gerard/  mailto:ger...@xray.bmc.uu.se
> **
>The opinions in this message are fictional.  Any similarity
>to actual opinions, living or dead, is purely coincidental.
> **
>

-- 

 ===
 * *
 * Gerard Bricogne g...@globalphasing.com  *
 * *
 * Global Phasing Ltd. *
 * Sheraton House, Castle Park Tel: +44-(0)1223-353033 *
 * Cambridge CB3 0AX, UK   Fax: +44-(0)1223-366889 *
 * *
 ===

Re: [ccp4bb] Secondary structure restraints

[Pete Meyer]

> to my knowledge, none of the existing reciprocal-space refinement
> programs is really suitable for low-resolution refinement. In my

For what it's worth, I've had good luck with refmac5D, which
incorporates an SAS target into model refinement (I believe this was has
now been incorporated into the mainstream refmac branch semi-recently).
 Making full use of the chemistry/geometry information is important, but
so is using as many observations as you can get your hands on.


Pete

Re: [ccp4bb] structure (factor) amplitude

[Gerard DVD Kleywegt]

As suggested by Tassos, what we need now more than ever is some Dutch 
diplomacy so that he healing can really begin. Various people have argued for 
a shorter term (Brazilians, Pflugrath) and since I'm personally rather partial 
to Brazilians I would say we ought to go with that and shave off a few 
letters.


So: we need a shorter, unambiguous term. I also think it should sound 
delicious. And it should be related to "structure (factor)" and "amplitude". 
We could take the first few letters of "STRucture", add some of the last ones 
of "amplitUDe". And to sweeten the deal (and reflecting the Austrian roots of 
Bernhard R and the Teutonic dittos of Jim P), we could add a diminutive "l". 
Thus we obtain:


 STRUDL

So can we agree that, from now on, |F| is refered to as "strudl"? Examples of 
usage:


- "I have deposited my experimental strudls and sigmas, boss!"

- "We calculated a SIGMAA-weighted map with coefficients two-m-strudl-obs 
minus D-strudl-calc."


N.B.: In the special case that the |F| are the result of AP (auto-processing) 
of FEL (free-electron laser) data, the appropriate term would obviously be: 
"APFELSTRUDL".


--DVD

**
   Gerard J.  Kleywegt
   Dept. of Cell & Molecular Biology  University of Uppsala
   Biomedical Centre  Box 596
   SE-751 24 Uppsala  SWEDEN

http://xray.bmc.uu.se/gerard/  mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**

Re: [ccp4bb] structure (factor) amplitude

[Robert Sweet]

Come on, Jim, even now 90% of students don't realize that F 
is a phased amplitude, we think of it as a complex number, and that F(obs) 
or F(calc) are probably the appropriate |F|.


Bob

On Mon, 12 Jan 2009, Jim Pflugrath wrote:

I wonder if the early use of the shortened "structure amplitude" is because 
it was a pain to do any typing, word processing, typesetting, etc before 
Gutenberg.


But soon crystallographers will be solving all their structures on their cell 
phones and also just text messaging manuscripts to editors and CCP4BB.  So we 
should probably be thinking of the newer shortened spelling of our scientific 
terms of the future.


Jim

PS: I vote for that "structure factor amplitude" be used in text books and 
|F| on cell phones.  Student of 2015: "You mean 'abs-F' is really pronounced 
'structure factor amplitude'?  I didn't know that!"




--
=
Robert M. Sweet E-Dress: sw...@bnl.gov
Group Leader, PXRR: Macromolecular   ^ (that's L
  Crystallography Research Resource at NSLSnot 1)
  http://px.nsls.bnl.gov/
Biology Dept
Brookhaven Nat'l Lab.   Phones:
Upton, NY  11973631 344 3401  (Office)
U.S.A.  631 344 2741  (Facsimile)
=

Re: [ccp4bb] structure (factor) amplitude

[Ethan Merritt]

On Monday 12 January 2009 10:45:30 Gerard Bricogne wrote:
> Dear Jacob and Jianghai,
> 
>  The trouble with this "King James version" is that what he calls the
> "structure amplitude" A is the amplitude of the scattered electromagnetic
> wave! If you look at equation (2.3) on p.27, the expression for A is first
> of all complex (!), and refers for each atom to its "scattering power",
> denoted phi[j]. This phi[j] is subsequently expressed in equation (2.11) in
> terms of some physical constants, of the squared atomic form factor, and of
> the polarisation factor, allowing A to be written in terms of the "structure
> factor" F defined in the familiar manner and of these other factors.
> 
>  Therefore, what Ewald and James call the "structure amplitude" is NOT
> AT ALL the amplitude (or modulus) of the structure factor, and therefore
> these venerable authors cannot be brought into the debate in this way! 
> 
> 
>  With best wishes,
>  
>   Gerard.


Very good point.
James' "structure amplitude" A is given by 

   A = -F(e^2/mc^2) cos(2theta)  eq. 2.12page 31

and he later refers to |F(hkl)| as the "geometrical structure factor"
(page 32), before amending its definition to note that it ignores
the effects of anomalous scattering.

"geometrical structure factor" gets 68 hits in the IUCr search engine,
and 2190 GHits   (GHits == Google Hits)


Ethan



> 
> --
> On Mon, Jan 12, 2009 at 12:58:27PM -0500, Jianghai Zhu wrote:
> > JPK beats me on this one.  Here is the quote from R. W. James, "The Optical 
> > Principles of the Diffraction of X-rays".
> >
> > "We shall call A the 'structure amplitude', a name introduced by Ewald, to 
> > denote the fact that its value depends essentially on the structure of the 
> > group associated with each lattice-point.  It is the amplitude, at unit 
> > distance, of the wave scattered by the unit group of s points."
> >
> > -- Jianghai
> >
> > 
> > Jianghai Zhu, PhD
> > Immune Disease Institute
> > Dept. of Pathology
> > Harvard Medical School
> > 3 Blackfan Circle, CLSB
> > Boston, MA 02115
> > Tel: 617-713-8224
> > Fax: 617-713-8232
> > 
> >
> >
> >
> >
> >
> >
> >
> > On Jan 12, 2009, at 12:43 PM, Jacob Keller wrote:
> >
> >> [King?] James says "structure amplitude."
> >>
> >> (1950 ed., Ch II, 1a (p27))
> >>
> >> JPK
> >>
> >> ***
> >> Jacob Pearson Keller
> >> Northwestern University
> >> Medical Scientist Training Program
> >> Dallos Laboratory
> >> F. Searle 1-240
> >> 2240 Campus Drive
> >> Evanston IL 60208
> >> lab: 847.491.2438
> >> cel: 773.608.9185
> >> email: j-kell...@northwestern.edu
> >> ***
> >>
> >> - Original Message - From: "Ethan Merritt" 
> >> 
> >> To: 
> >> Sent: Monday, January 12, 2009 10:59 AM
> >> Subject: Re: [ccp4bb] structure (factor) amplitude
> >>
> >>
> >>> On Monday 12 January 2009 02:42:43 Ian Tickle wrote:
> >>>
>  Also I did a 'Google vote' for the two terms.  'Structure amplitude' has
>  11300 hits.  'Structure factor amplitude' has only 4750.  So all round I
>  would say that 'structure amplitude' wins by a considerable margin.
> >>>
> >>> The field of crystagooglography is relatively young,
> >>> and standard procedures have not yet been established :-)
> >>> Here's what I get:
> >>>
> >>> +"structure factor amplitude"  18,000 hits
> >>> +"structure amplitude" 17,100 hits
> >>>
> >>> Ethan
> >>>
> >>>
> 
>  Cheers
> 
>  -- Ian
> 
>  > -Original Message-
>  > From: owner-ccp...@jiscmail.ac.uk
>  > [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Pavel Afonine
>  > Sent: 11 January 2009 03:01
>  > To: Ethan A Merritt
>  > Cc: CCP4BB@jiscmail.ac.uk
>  > Subject: Re: [ccp4bb] structure (factor) amplitude
>  >
>  >
>  >
>  > On 1/10/2009 5:14 PM, Ethan A Merritt wrote:
>  >
>  > On Saturday 10 January 2009, Bernhard Rupp wrote:
>  >
>  >
>  > Dear All,
>  >
>  > I am getting conflicting comments on the use of
>  > 'structure factor amplitude'
>  > vs. just
>  > 'structure amplitude'
>  > for |F|.
>  >
>  >
>  >
>  > ???
>  > That's just... odd.
>  >
>  > |F| is the amplitude of F.
>  > But no way F is a "structure".
>  >
>  >
>  >
>  > I agree. If F is a structure factor then |F| is a structure
>  > factor amplitude. "structure amplitude" doesn't make much sense...
>  > Pavel.
> 
> 
>  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 ha

Re: [ccp4bb] structure (factor) amplitude

[Jianghai Zhu]

Gerard,

You are absolutely right.  My apology for the confusion.  Keep on  
reading, looks like that James called |F| "geometrical structure  
factor", which probably is not commonly used anymore.


-- Jianghai






On Jan 12, 2009, at 1:45 PM, Gerard Bricogne wrote:


Dear Jacob and Jianghai,

The trouble with this "King James version" is that what he calls  
the
"structure amplitude" A is the amplitude of the scattered  
electromagnetic
wave! If you look at equation (2.3) on p.27, the expression for A is  
first
of all complex (!), and refers for each atom to its "scattering  
power",
denoted phi[j]. This phi[j] is subsequently expressed in equation  
(2.11) in
terms of some physical constants, of the squared atomic form factor,  
and of
the polarisation factor, allowing A to be written in terms of the  
"structure

factor" F defined in the familiar manner and of these other factors.

Therefore, what Ewald and James call the "structure amplitude"  
is NOT
AT ALL the amplitude (or modulus) of the structure factor, and  
therefore

these venerable authors cannot be brought into the debate in this way!


With best wishes,

 Gerard.

--
On Mon, Jan 12, 2009 at 12:58:27PM -0500, Jianghai Zhu wrote:
JPK beats me on this one.  Here is the quote from R. W. James, "The  
Optical

Principles of the Diffraction of X-rays".

"We shall call A the 'structure amplitude', a name introduced by  
Ewald, to
denote the fact that its value depends essentially on the structure  
of the
group associated with each lattice-point.  It is the amplitude, at  
unit

distance, of the wave scattered by the unit group of s points."

-- Jianghai


Jianghai Zhu, PhD
Immune Disease Institute
Dept. of Pathology
Harvard Medical School
3 Blackfan Circle, CLSB
Boston, MA 02115
Tel: 617-713-8224
Fax: 617-713-8232








On Jan 12, 2009, at 12:43 PM, Jacob Keller wrote:


[King?] James says "structure amplitude."

(1950 ed., Ch II, 1a (p27))

JPK

***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.491.2438
cel: 773.608.9185
email: j-kell...@northwestern.edu
***

- Original Message - From: "Ethan Merritt"

To: 
Sent: Monday, January 12, 2009 10:59 AM
Subject: Re: [ccp4bb] structure (factor) amplitude



On Monday 12 January 2009 02:42:43 Ian Tickle wrote:

Also I did a 'Google vote' for the two terms.  'Structure  
amplitude' has
11300 hits.  'Structure factor amplitude' has only 4750.  So all  
round I
would say that 'structure amplitude' wins by a considerable  
margin.


The field of crystagooglography is relatively young,
and standard procedures have not yet been established :-)
Here's what I get:

+"structure factor amplitude"  18,000 hits
+"structure amplitude" 17,100 hits

Ethan




Cheers

-- Ian


-Original Message-
From: owner-ccp...@jiscmail.ac.uk
[mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Pavel Afonine
Sent: 11 January 2009 03:01
To: Ethan A Merritt
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] structure (factor) amplitude



On 1/10/2009 5:14 PM, Ethan A Merritt wrote:

On Saturday 10 January 2009, Bernhard Rupp wrote:


Dear All,

I am getting conflicting comments on the use of
'structure factor amplitude'
vs. just
'structure amplitude'
for |F|.



???
That's just... odd.

|F| is the amplitude of F.
But no way F is a "structure".



I agree. If F is a structure factor then |F| is a structure
factor amplitude. "structure amplitude" doesn't make much  
sense...

Pavel.



Disclaimer
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Re: [ccp4bb] X-Stream 2000 problem - ICING

[mjvdwoerd]

 Mark,

What bothers me about your message is that you already have talked to Rigaku. 
Until now we have never been able to create a problem that they could not 
diagnose and help me solve from remote. In danger of offending ccp4 readers: 
specialized Rigaku experts are a remarkable source for information and 
solutions, probably better than we are.

Your most likely problem is that your nitrogen is not dry? Specifically, check 
your air dryer (sorry, nitrogen dryer) that it works appropriately. Very 
specifically, there reside two compressors inside the air dryer and if one no 
longer works, the quality of your nitrogen stream degrades. It may not be 
apparent if both compressors work, one can supply all the pressure and volume 
you need and is sufficiently noisy that you would not notice the second being 
silent. Of course this problem becomes obvious when you open up the cabinet. 
(Yes, of course this happened to us once before and in our case the compressor 
wiring was fickle, as in, working when the cabinet was open and not (always) 
working when the cabinet was closed; took FOREVER to find the problem.)

Your second most likely reason is that the warm stream (outer stream) is not 
sufficiently protecting your cold stream from humidity, but this is not 
affected by your phi-axis position. We have two inverted phi-axes and we do not 
see icing, so there is no fundamental reason why the phi-axis should not be 
inverted.

Mark
? 


 


 

-Original Message-
From: Mark Agacan 
To: CCP4BB@JISCMAIL.AC.UK
Sent: Mon, 12 Jan 2009 3:42 am
Subject: [ccp4bb] X-Stream 2000 problem - ICING










Apologies for this slightly off topic question:  

I am having a great deal of trouble with my X-Stream 2000 cryostream system and 
I wondered if other users have similar problems.  

I've replaced almost all components (new GAST compressors, helium recharges, 
filters, etc., etc.) in the last couple of months but there is almost always 
icing of any cryo within 10 - 20 minutes of mounting a loop, and it is 
adversely 
affecting data collections.  

It appears like there is too much moisture in the cold or wam streams but the 
tubes have been fully dried out as per Rigaku advice.  

This X-Stream is attached to a generator with inverted phi axis and and i'm 
wondering if this could be the source of the problem, as the X-Stream for 
another generator in the same laboratory with normal phi axis does not ice up.  
Can some sort of turbulence around the loop caused by backdraft from the cryo 
hitting the inverted phi axis / camera mount cause excess humidity and lead to 
icing on the pin, loop and crystal?  

Has anyone else got this problem?  Any suggestions would be very gratefully 
appreciated.

Best Wishes,

Mark


_
Dr Mark Agacan
Scientific Officer,
Division of Biological Chemistry 
and Drug Discovery,
Wellcome Trust Biocentre,
College of Life Sciences,
Dow St., 
University of Dundee,
Dundee, DD1 5EH
Tel: +44 1382 388751
Fax: +44 1382 345764
_
The University of Dundee is a registered Scottish charity, No: SC015096



 

Re: [ccp4bb] structure (factor) amplitude

[Gerard Bricogne]

Dear Jacob and Jianghai,

 The trouble with this "King James version" is that what he calls the
"structure amplitude" A is the amplitude of the scattered electromagnetic
wave! If you look at equation (2.3) on p.27, the expression for A is first
of all complex (!), and refers for each atom to its "scattering power",
denoted phi[j]. This phi[j] is subsequently expressed in equation (2.11) in
terms of some physical constants, of the squared atomic form factor, and of
the polarisation factor, allowing A to be written in terms of the "structure
factor" F defined in the familiar manner and of these other factors.

 Therefore, what Ewald and James call the "structure amplitude" is NOT
AT ALL the amplitude (or modulus) of the structure factor, and therefore
these venerable authors cannot be brought into the debate in this way! 


 With best wishes,
 
  Gerard.

--
On Mon, Jan 12, 2009 at 12:58:27PM -0500, Jianghai Zhu wrote:
> JPK beats me on this one.  Here is the quote from R. W. James, "The Optical 
> Principles of the Diffraction of X-rays".
>
> "We shall call A the 'structure amplitude', a name introduced by Ewald, to 
> denote the fact that its value depends essentially on the structure of the 
> group associated with each lattice-point.  It is the amplitude, at unit 
> distance, of the wave scattered by the unit group of s points."
>
> -- Jianghai
>
> 
> Jianghai Zhu, PhD
> Immune Disease Institute
> Dept. of Pathology
> Harvard Medical School
> 3 Blackfan Circle, CLSB
> Boston, MA 02115
> Tel: 617-713-8224
> Fax: 617-713-8232
> 
>
>
>
>
>
>
>
> On Jan 12, 2009, at 12:43 PM, Jacob Keller wrote:
>
>> [King?] James says "structure amplitude."
>>
>> (1950 ed., Ch II, 1a (p27))
>>
>> JPK
>>
>> ***
>> Jacob Pearson Keller
>> Northwestern University
>> Medical Scientist Training Program
>> Dallos Laboratory
>> F. Searle 1-240
>> 2240 Campus Drive
>> Evanston IL 60208
>> lab: 847.491.2438
>> cel: 773.608.9185
>> email: j-kell...@northwestern.edu
>> ***
>>
>> - Original Message - From: "Ethan Merritt" 
>> 
>> To: 
>> Sent: Monday, January 12, 2009 10:59 AM
>> Subject: Re: [ccp4bb] structure (factor) amplitude
>>
>>
>>> On Monday 12 January 2009 02:42:43 Ian Tickle wrote:
>>>
 Also I did a 'Google vote' for the two terms.  'Structure amplitude' has
 11300 hits.  'Structure factor amplitude' has only 4750.  So all round I
 would say that 'structure amplitude' wins by a considerable margin.
>>>
>>> The field of crystagooglography is relatively young,
>>> and standard procedures have not yet been established :-)
>>> Here's what I get:
>>>
>>> +"structure factor amplitude"  18,000 hits
>>> +"structure amplitude" 17,100 hits
>>>
>>> Ethan
>>>
>>>

 Cheers

 -- Ian

 > -Original Message-
 > From: owner-ccp...@jiscmail.ac.uk
 > [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Pavel Afonine
 > Sent: 11 January 2009 03:01
 > To: Ethan A Merritt
 > Cc: CCP4BB@jiscmail.ac.uk
 > Subject: Re: [ccp4bb] structure (factor) amplitude
 >
 >
 >
 > On 1/10/2009 5:14 PM, Ethan A Merritt wrote:
 >
 > On Saturday 10 January 2009, Bernhard Rupp wrote:
 >
 >
 > Dear All,
 >
 > I am getting conflicting comments on the use of
 > 'structure factor amplitude'
 > vs. just
 > 'structure amplitude'
 > for |F|.
 >
 >
 >
 > ???
 > That's just... odd.
 >
 > |F| is the amplitude of F.
 > But no way F is a "structure".
 >
 >
 >
 > I agree. If F is a structure factor then |F| is a structure
 > factor amplitude. "structure amplitude" doesn't make much sense...
 > Pavel.


 Disclaimer
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 information intended solely for the named addressee(s). It may not be 
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 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 i.tic...@astex-therapeutics.com 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 L

Re: [ccp4bb] structure (factor) amplitude

[Ian Tickle]

Well according to Google this paper (JCS, 1936) contains the phrase
"magnitudes of the structure amplitude factors (F)":

http://www.google.co.uk/search?hl=en&q=%22magnitudes+of+the+structure+am
plitude+factors%22&btnG=Search&meta= .

It seems that "structure amplitude factor" is what we have now
abbreviated to "structure factor", i.e. it would appear that "amplitude"
was being used in a different sense from what we are using.  Logically
the magnitude of a structure amplitude factor should be a "structure
amplitude factor magnitude", so I guess it was not surprising that it
was abbreviated to just "structure amplitude".  I hardly think you could
call it a "structure amplitude factor amplitude"!

-- Ian

> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk 
> [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Bernhard Rupp
> Sent: 12 January 2009 17:44
> To: CCP4BB@JISCMAIL.AC.UK; sa...@igbmc.fr
> Subject: Re: [ccp4bb] structure (factor) amplitude
> 
> Hmmm.
> 
> Sacha just threw another wrench into that discourse. Seems we are
> also faced with a duality problem here:
> 
> Coming from a mathematical point of view treating F as a 
> complex number,
> 
> structure factor magnitude or 
> structure factor modulus
>  
> is more logical and more direct.
> 
> If you are taking the physical pov (let's not go into detail 
> there, btw)
> *interpreting* the complex number as wave description
> (and here I must say Ian's point wrt song title/name is well taken)  
> 
> structure factor amplitude 
> 
> is more logical.
> 
> Best, BR
> 
> Dear Bernhard,
> 
> First of all, happy new year !
> 
>  > I am getting conflicting comments on the use of
>  > 'structure factor amplitude'
>  > vs. just
>  > 'structure amplitude' for |F|.
> 
> Even when "structure factor amplitude" (or "magnitude", 
> following some 
> english-speaking persons?? If I am right I learned that 
> M.Woolfson prefers 
> "magnitude". My English is too poor to judge) seems to be 
> long, it seems to 
> be correct and have a clear meaning. That is not the case for 
> "structure 
> amplitude". In that sens I agree with Ethan and Pavel.
> 
> With best wishes !
> 
> Sacha
> 
> 


Disclaimer
This communication is confidential and may contain privileged information 
intended solely for the named addressee(s). It may not be used or disclosed 
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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 
i.tic...@astex-therapeutics.com 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 
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Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, 
Cambridge CB4 0QA under number 3751674

Re: [ccp4bb] structure (factor) amplitude

[Jianghai Zhu]

JPK beats me on this one.  Here is the quote from R. W. James, "The  
Optical Principles of the Diffraction of X-rays".


"We shall call A the 'structure amplitude', a name introduced by  
Ewald, to denote the fact that its value depends essentially on the  
structure of the group associated with each lattice-point.  It is the  
amplitude, at unit distance, of the wave scattered by the unit group  
of s points."


-- Jianghai


Jianghai Zhu, PhD
Immune Disease Institute
Dept. of Pathology
Harvard Medical School
3 Blackfan Circle, CLSB
Boston, MA 02115
Tel: 617-713-8224
Fax: 617-713-8232








On Jan 12, 2009, at 12:43 PM, Jacob Keller wrote:


[King?] James says "structure amplitude."

(1950 ed., Ch II, 1a (p27))

JPK

***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.491.2438
cel: 773.608.9185
email: j-kell...@northwestern.edu
***

- Original Message - From: "Ethan Merritt" >

To: 
Sent: Monday, January 12, 2009 10:59 AM
Subject: Re: [ccp4bb] structure (factor) amplitude



On Monday 12 January 2009 02:42:43 Ian Tickle wrote:

Also I did a 'Google vote' for the two terms.  'Structure  
amplitude' has
11300 hits.  'Structure factor amplitude' has only 4750.  So all  
round I

would say that 'structure amplitude' wins by a considerable margin.


The field of crystagooglography is relatively young,
and standard procedures have not yet been established :-)
Here's what I get:

+"structure factor amplitude"  18,000 hits
+"structure amplitude" 17,100 hits

Ethan




Cheers

-- Ian

> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk
> [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Pavel Afonine
> Sent: 11 January 2009 03:01
> To: Ethan A Merritt
> Cc: CCP4BB@jiscmail.ac.uk
> Subject: Re: [ccp4bb] structure (factor) amplitude
>
>
>
> On 1/10/2009 5:14 PM, Ethan A Merritt wrote:
>
> On Saturday 10 January 2009, Bernhard Rupp wrote:
>
>
> Dear All,
>
> I am getting conflicting comments on the use of
> 'structure factor amplitude'
> vs. just
> 'structure amplitude'
> for |F|.
>
>
>
> ???
> That's just... odd.
>
> |F| is the amplitude of F.
> But no way F is a "structure".
>
>
>
> I agree. If F is a structure factor then |F| is a structure
> factor amplitude. "structure amplitude" doesn't make much sense...
> Pavel.


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 i.tic...@astex-therapeutics.com 
 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






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

Re: [ccp4bb] structure (factor) amplitude

[Bernhard Rupp]

Hmmm.

Sacha just threw another wrench into that discourse. Seems we are
also faced with a duality problem here:

Coming from a mathematical point of view treating F as a complex number,

structure factor magnitude or 
structure factor modulus
 
is more logical and more direct.

If you are taking the physical pov (let's not go into detail there, btw)
*interpreting* the complex number as wave description
(and here I must say Ian's point wrt song title/name is well taken)  

structure factor amplitude 

is more logical.

Best, BR

Dear Bernhard,

First of all, happy new year !

 > I am getting conflicting comments on the use of
 > 'structure factor amplitude'
 > vs. just
 > 'structure amplitude' for |F|.

Even when "structure factor amplitude" (or "magnitude", following some 
english-speaking persons?? If I am right I learned that M.Woolfson prefers 
"magnitude". My English is too poor to judge) seems to be long, it seems to 
be correct and have a clear meaning. That is not the case for "structure 
amplitude". In that sens I agree with Ethan and Pavel.

With best wishes !

Sacha

Re: [ccp4bb] structure (factor) amplitude

[Jacob Keller]

[King?] James says "structure amplitude."

(1950 ed., Ch II, 1a (p27))

JPK

***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.491.2438
cel: 773.608.9185
email: j-kell...@northwestern.edu
***

- Original Message - 
From: "Ethan Merritt" 

To: 
Sent: Monday, January 12, 2009 10:59 AM
Subject: Re: [ccp4bb] structure (factor) amplitude



On Monday 12 January 2009 02:42:43 Ian Tickle wrote:


Also I did a 'Google vote' for the two terms.  'Structure amplitude' has
11300 hits.  'Structure factor amplitude' has only 4750.  So all round I
would say that 'structure amplitude' wins by a considerable margin.


The field of crystagooglography is relatively young,
and standard procedures have not yet been established :-)
Here's what I get:

+"structure factor amplitude"  18,000 hits
+"structure amplitude" 17,100 hits

Ethan




Cheers

-- Ian

> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk
> [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Pavel Afonine
> Sent: 11 January 2009 03:01
> To: Ethan A Merritt
> Cc: CCP4BB@jiscmail.ac.uk
> Subject: Re: [ccp4bb] structure (factor) amplitude
>
>
>
> On 1/10/2009 5:14 PM, Ethan A Merritt wrote:
>
> On Saturday 10 January 2009, Bernhard Rupp wrote:
>
>
> Dear All,
>
> I am getting conflicting comments on the use of
> 'structure factor amplitude'
> vs. just
> 'structure amplitude'
> for |F|.
>
>
>
> ???
> That's just... odd.
>
> |F| is the amplitude of F.
> But no way F is a "structure".
>
>
>
> I agree. If F is a structure factor then |F| is a structure
> factor amplitude. "structure amplitude" doesn't make much sense...
> Pavel.


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 i.tic...@astex-therapeutics.com 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






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

[ccp4bb] Deadline for ALS PX beamtime this Thursday, Jan 15.

[Peter Zwart]

Dear All,

The deadline for general user proposals for PX beamtime at the ALS is
coming up soon (Jan 15)! At the BCSB, we have 5 beamlines for which you can
apply for beamtime. At the Berkeley Center for Structural Biology
(BCSB) we have recently completed a number of upgrades:

Sector 8:  Recent improvements include:

   * A high-accuracy microdiffractometer on BL 8.2.1, allowing for
  centering and viewing of very small crystals
   * Robotic automounters which can increase the screening throughput
 at the beamlines, and allows for the implementation of remote data
 collection.
   * A new large format (315mm active surface area) CCD detector on
 BL 8.2.1, facilitating data collection on large unit cell crystals

 Sector 5:  Beamlines (5.0.1 and 5.0.3) now generate 1.5x10^11 photons
 per second at 0.97 Angstrom. This wavelength is slightly above the Se
 K edge making them ideal for performing Se SAD experiments. Beamline
 5.0.2 (the tunable beamline) generates a peak flux of 8x10^11 photons
 per second, and the energy range of 5.0.2 has been extended to 17 keV,
 enabling the routine use of shorter wavelengths and anomalously
 scattering elements such as bromine.
 Remote data collection for general users on sector 5 is currently
 being tested for a limited number of users. Please contact beamline
staff for details.

 Please visit http://bcsb.lbl.gov/ for more details about the Center
 and its beamlines.

 If you'd like to apply for next round of beamtime (March-April) at the
 Advanced Light Source, please submit a General User proposal by
Januari 15, 2009.

 To find out more, click on:

 http://www-als.lbl.gov/als/quickguide/independinvest.html

 We invite you to submit a proposal at:

http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml/Initialize


If you have any questions or would like to request open beamtime,
please e-mail bcsbbeamt...@lbl.gov.

(Please note that executed user agreements must be received by LBNL
prior to beamtime.  Proprietary fees, if applicable, must be received
by LBNL at least five working days prior to scheduled beamtime.)


-
P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB: http://bcsb.als.lbl.gov
PHENIX: http://www.phenix-online.org
CCTBX:  http://cctbx.sf.net
-

Re: [ccp4bb] structure (factor) amplitude

[Ethan Merritt]

On Monday 12 January 2009 02:42:43 Ian Tickle wrote:

> Also I did a 'Google vote' for the two terms.  'Structure amplitude' has
> 11300 hits.  'Structure factor amplitude' has only 4750.  So all round I
> would say that 'structure amplitude' wins by a considerable margin.

The field of crystagooglography is relatively young,
and standard procedures have not yet been established :-)  
Here's what I get:

+"structure factor amplitude"  18,000 hits
+"structure amplitude" 17,100 hits

Ethan


> 
> Cheers
> 
> -- Ian
> 
> > -Original Message-
> > From: owner-ccp...@jiscmail.ac.uk 
> > [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Pavel Afonine
> > Sent: 11 January 2009 03:01
> > To: Ethan A Merritt
> > Cc: CCP4BB@jiscmail.ac.uk
> > Subject: Re: [ccp4bb] structure (factor) amplitude
> > 
> > 
> > 
> > On 1/10/2009 5:14 PM, Ethan A Merritt wrote: 
> > 
> > On Saturday 10 January 2009, Bernhard Rupp wrote:
> >   
> > 
> > Dear All,
> > 
> > I am getting conflicting comments on the use of 
> > 'structure factor amplitude'
> > vs. just
> > 'structure amplitude'
> > for |F|.
> > 
> > 
> > 
> > ???
> > That's just... odd.
> > 
> > |F| is the amplitude of F.
> > But no way F is a "structure".
> >   
> > 
> > 
> > I agree. If F is a structure factor then |F| is a structure 
> > factor amplitude. "structure amplitude" doesn't make much sense...
> > Pavel.
> 
> 
> 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 
> i.tic...@astex-therapeutics.com 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
> 



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

[ccp4bb] Postdoctoral opportunities at University of Pittsburgh

[Laurie Betts]

Post-doctoral positions in macromolecular crystallography and NMR  
spectroscopy at the University of Pittsburgh in the Department of  
Structural Biology. There are several postdoctoral positions available  
immediately, with opportunities to work in projects related to  
Metabolic Membrane Proteins and to the Pittsburgh Center for HIV  
Protein Interactions (http://www2.structbio.pitt.edu/hivppi/site/index.php 
).  These positions are in the laboratory of Professors Angela M.  
Gronenborn (NMR/X-ray) and Joanne I. Yeh (Macromolecular X-ray  
crystallography).



The resources for X-ray Crystallography and NMR spectroscopy are  
outstanding. The X-ray Crystallography Facility includes automated  
crystallization screening and imaging, two high flux rotating anode  
generators, two CCD and two image plate detectors, and access to  
synchrotron time at SER-CAT; additional information can be found at (http://www2.structbio.pitt.edu/hivppi/site/cores_xray.php 
). The NMR facility (http://www.structbio.pitt.edu/drupal-5/?q=nmr)  
comprises of a total of six spectrometers dedicated to biological NMR.  
These include three 600 MHz spectrometers, 700 MHz, 800 MHz and 900  
MHz spectrometers. All spectrometers are fully equipped with hardware  
for all modern multinuclear experiments including triple-axis  
gradients and the capability for multi-channel pulsing with deuterium  
decoupling. Cryoprobes have been installed at every field strength.



Candidates should have a Ph.D. in structural biology or related fields  
(Chemistry, Physics, Biochemistry, Biophysics, Molecular Biology);  
experience in biological NMR or macromolecular crystal structure  
determination, including protein crystallization, data collection/ 
processing, structure determination and model refinement a plus.  
Please direct inquiries; or send your CV and the names and contact  
information for three references to Ms. Janet Zambotti (NMR) or Dr.  
Laurie Betts (X-ray crystallography) to the following e-mail address:



Laurie Betts
X-ray Crystallography Facility Manager
Department of Structural Biology
University of Pittsburgh
3501 Fifth Avenue 1047 BST3
Pittsburgh, PA 15260
412-383-5839
Email:  lab...@pitt.edu

Janet Zambotti
Assistant to Angela M. Gronenborn
Department of Structural Biology
University of Pittsburgh School of Medicine
3501 Fifth Avenue, 1047 BST3
Pittsburgh, PA  15260
Telephone – 412/648-9866
Email – zambo...@pitt.edu

[ccp4bb] arp/warp 7.0.1 and ccp4i

[Petr Leiman]

Hello all,

While testing a newly installed ARP/wARP interface (ver. 7.0.1) in ccp4i 
(ver. 6.1.0) on Ubuntu (8.10) I noticed that the Fobs and Sigma pull-down 
menus are missing from the ARP/wARP Quick Fold window. This is accompanied 
by the following error message, which is output in stderr by the ccp4i 
interface:

ERROR  CreateLabinLine:  unrecognised argument -fileout

To remedy this problem one has to edit the
warp_albe.tcl
file, which is located in $CCP4/ccp4i/tasks  directory.

Line 325
-fileout XYZOUT DIR_XYZOUT "_helices_"
has to be removed.

All the best,

Petr

Re: [ccp4bb] structure (factor) amplitude

[mesters]

Not only in Stout & Jensen but also in Blundell & Johnson 1976, Jan 
Drenth's book and many more use "structure amplitude".


I like to think that "structure amplitude" (would not dare to call it 
"slang") is the crystallographers short form of "structure factor 
amplitude".
Although all of us know what is meant, for a novice to the field (and 
the broader audience) "structure factor amplitude" would be the correct 
term to use.


- J. -


Sue Roberts wrote:
My preference is also for the full structure factor amplitude.  I 
would have said that I'd never seen the term structure amplitude used.


However, I just looked this up in my old Stout & Jensen (1968 edition 
- brown cover) and find that (on p. 195) where |F| is introduced they 
define it as: 'the most important quantity derived from the 
intensities is the /structure factor modulus (structure amplitude)/.   
(Italics are theirs, not mine).


Sue

On Jan 12, 2009, at 8:37 AM, Andrew Purkiss-Trew wrote:


On Mon, 2009-01-12 at 10:42 +, Ian Tickle wrote:

I was taught 'structure amplitude' - makes perfect sense to me!  Why
does 'structure amplitude' make any less sense than 'structure factor'?

It also clearly made sense to Phil Coppens, a crystallographer of
considerable repute, see ITC Vol. B (2nd Ed.), sect 1.2., p.10: 'The
Structure Factor'.  To quote the introduction to the section: "The
'structure factor' is the central concept in structure analysis by
diffraction methods.  Its modulus is called the 'structure amplitude'".

Also I did a 'Google vote' for the two terms.  'Structure amplitude' has
11300 hits.  'Structure factor amplitude' has only 4750.  So all round I
would say that 'structure amplitude' wins by a considerable margin.



Having had a quick look at the google results myself, I think that there
is a problem is the methodology. Google doesn't take into account
punctuation when searching. So the first search includes results such as
'structure. Amplitude', where the two words are in different sentences,
or 'structure, amplitude' where the words are part of a list. Given this
case, the winning margin is likely to be less.

My preference would also be for the full 'Structure factor amplitude'.
'Structure amplitude' leaves me with visions of comparing the pdb files
of a small single domain protein and a ribosome. Two structures having
different sizes (or amplitudes).


Cheers

-- Ian


-Original Message-
From: owner-ccp...@jiscmail.ac.uk 
[mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Pavel Afonine
Sent: 11 January 2009 03:01
To: Ethan A Merritt
Cc: CCP4BB@jiscmail.ac.uk 
Subject: Re: [ccp4bb] structure (factor) amplitude



On 1/10/2009 5:14 PM, Ethan A Merritt wrote:

On Saturday 10 January 2009, Bernhard Rupp wrote:
 


Dear All,

I am getting conflicting comments on the use of
'structure factor amplitude'
vs. just
'structure amplitude'
for |F|.
   



???
That's just... odd.

|F| is the amplitude of F.
But no way F is a "structure".
 



I agree. If F is a structure factor then |F| is a structure
factor amplitude. "structure amplitude" doesn't make much sense...
Pavel.



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 i.tic...@astex-therapeutics.com 
 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




Dr. Sue A. Roberts
Biochemistry & Molecular Biophysics
University of Arizona
520 621 8171
s...@email.arizona.edu 
http://www.biochem.arizona.edu/xray










--
Dr. Jeroen R. Mesters
Gruppenleiter Strukturelle Neu

Re: [ccp4bb] 2D

[Vin Purp]

 Hi, 
Thanks for the suggestion. Here is more info: It is a soluble protein, a 
monomer has 3alpha and 3 beta subunits, and exists in solution as a dimer. The 
technique is hanging drop, vapor diffusion.? And the? mother liquor is ~ 0.1 mM 
cacodylate pH 6.2ish, MgCl2 and PEG 20k. 

=v=


 


 

-Original Message-
From: Puey Ounjai 
To: CCP4BB@JISCMAIL.AC.UK
Sent: Fri, 9 Jan 2009 3:56 pm
Subject: Re: [ccp4bb] 2D










Hello,
The information you provided to us here is not enough. there are so many 
parameters and 
so many means to optimize 2D crystal. All of which depends on what kind of 
protein you 
are working on (membrane associated or soluble) and what kind of technique that 
you use 
to grow your crystal (lipid monolayer, dialysis or else).

I guess unless you give us more info about your crystal otherwise it will be 
quite difficult 
for us to help you optimize your condition.

Sincerely,
Puey 



 

Re: [ccp4bb] structure (factor) amplitude

[Ian Tickle]

OK, limiting the vote to people whom I think we can assume know what
vaguely they're talking about, i.e. Acta Cryst. / J. Appl. Cryst.
authors, and using the IUCr search engine we get 553 hits for "structure
amplitude" and 256 for "structure factor amplitude" (quite close to the
ratio for Google so I don't think it's that far out).  I didn't check on
the peculiar quirks of the IUCr search engine re punctuation though
(believe it or not I have more important things to do!).

The earliest AC paper I can find mentioning "structure amplitude" is
this one from the Cavendish here in Cambridge published in 1948:
http://journals.iucr.org/q/issues/1948/05/00/a00073/a00073.pdf i.e. vol
1: you can't get any earlier than that, so the term must have been in
use before that, maybe even going back to the 1930's and the Braggs.

The earliest AC paper I can find mentioning "structure factor amplitude"
is this one from AERE Harwell in 1959:
http://journals.iucr.org/q/issues/1959/09/00/a02617/a02617.pdf .

The latest paper was 2008 in both cases.  So anyway clearly both terms
have been in use in parallel for many years, so the least you can say is
that either is acceptable.

Interestingly the authors of this paper:
http://journals.iucr.org/d/issues/2004/12/01/ba5067/ba5067.pdf maybe
decided to play it safe and used the term "structure amplitude" 5 times
against "structure factor amplitude" 16 times (clearly bucking the
majority trend!).  I think all one can conclude from that is that both
terms are equally clear to the majority of authors and readers alike.

Cheers

-- Ian

> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk 
> [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Ed Pozharski
> Sent: 12 January 2009 14:37
> To: Ian Tickle
> Cc: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] structure (factor) amplitude
> 
> > Also I did a 'Google vote' for the two terms.  'Structure 
> amplitude' has
> > 11300 hits.  'Structure factor amplitude' has only 4750.  
> So all round I
> > would say that 'structure amplitude' wins by a considerable margin.
> 
> 
> Results of another Google vote:
> 
> "Earth is flat":  
>   55,100,000 hits
> "Earth is round":
>   53,600,000 hits
> 
> Take that, Galileo, Columbus and Magellan!*
> 
> Of course, this post of mine is utterly irrelevant, just like all my
> other posts.  Just emphasizing that majority is not always right. 
> 
> *The vote is close enough to trigger an automatic recount, but Vatican
> has already declared victory and called on its opponents to concede so
> that the healing process may begin.
> 
> -- 
> Edwin Pozharski, PhD, Assistant Professor
> University of Maryland, Baltimore
> --
> When the Way is forgotten duty and justice appear;
> Then knowledge and wisdom are born along with hypocrisy.
> When harmonious relationships dissolve then respect and 
> devotion arise;
> When a nation falls to chaos then loyalty and patriotism are born.
> --   / Lao Tse /
> 
> 


Disclaimer
This communication is confidential and may contain privileged information 
intended solely for the named addressee(s). It may not be used or disclosed 
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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 
i.tic...@astex-therapeutics.com 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 
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Cambridge CB4 0QA under number 3751674

Re: [ccp4bb] structure (factor) amplitude

[Karsten . Niefind]

> 
> My preference is also for the full structure factor amplitude. I would have 
> said that I'd never seen 
> the term structure amplitude used. However, I just looked this up in my old 
> Stout & Jensen (1968 
> edition - brown cover) and find that (on p. 195) where |F| is introduced they 
> define it as: 'the most 
> important quantity derived from the intensities is the structure factor 
> modulus (structure 
> amplitude).  (Italics are theirs, not mine). 
> Sue 

Dear experts,

what about the phases? Should they termed "structure phases"?

Karsten Niefind

Re: [ccp4bb] structure (factor) amplitude

[Jim Pflugrath]

I wonder if the early use of the shortened "structure amplitude" is 
because it was a pain to do any typing, word processing, typesetting, etc 
before Gutenberg.


But soon crystallographers will be solving all their structures on their 
cell phones and also just text messaging manuscripts to editors and 
CCP4BB.  So we should probably be thinking of the newer shortened 
spelling of our scientific terms of the future.


Jim

PS: I vote for that "structure factor amplitude" be used in text books and 
|F| on cell phones.  Student of 2015: "You mean 'abs-F' is really 
pronounced 'structure factor amplitude'?  I didn't know that!"

[ccp4bb] composite omit map calculation

[Vineet Gaur]

  Hi All,
Sorry for a non CCP4 querry.
 I am using CNS for composite omit map calculations. the structure is having
a ligand for which parameter and topology files have been generated using
PRODRG server. however while running composite_omit_map.inp i m getting the
following torsion topology error (where chain D is the ligand):


"ERROR: There are no suitable base groups.
   This problem can be caused by isolated
   bonding networks with undefined or weak
   dihedral force constants.
   The atoms that cannot be placed in a tree
   are listed below:
%atoms "D   "-242 -AMG -O4
%atoms "D   "-242 -AMG -C4
%atoms "D   "-242 -AMG -C3
%atoms "D   "-242 -AMG -O3
%atoms "D   "-242 -AMG -C2
%atoms "D   "-242 -AMG -O2
%atoms "D   "-242 -AMG -C1
%atoms "D   "-242 -AMG -O1
%atoms "D   "-242 -AMG -C7
%atoms "D   "-242 -AMG -O5
%atoms "D   "-242 -AMG -C5
%atoms "D   "-242 -AMG -C6
%atoms "D   "-242 -AMG -O6
 %TORSION:TOPOLOGY error encountered: Fatal Topology Error
   (CNS is in mode: SET ABORT=NORMal END)
 *
 ABORT mode will terminate program execution.
 *
 Program will stop immediately."



topology and parameter files have been attached to this posting.

Kindly suggest if there is any problem with topology or parameter file or i
am missing on something else.

with best regards

Vineet Gaur


mam.param
Description: Binary data


mam.top
Description: Binary data

Re: [ccp4bb] structure (factor) amplitude

[Sue Roberts]

My preference is also for the full structure factor amplitude.  I  
would have said that I'd never seen the term structure amplitude used.


However, I just looked this up in my old Stout & Jensen (1968 edition  
- brown cover) and find that (on p. 195) where |F| is introduced they  
define it as: 'the most important quantity derived from the  
intensities is the structure factor modulus (structure amplitude).
(Italics are theirs, not mine).


Sue

On Jan 12, 2009, at 8:37 AM, Andrew Purkiss-Trew wrote:


On Mon, 2009-01-12 at 10:42 +, Ian Tickle wrote:

I was taught 'structure amplitude' - makes perfect sense to me!  Why
does 'structure amplitude' make any less sense than 'structure  
factor'?


It also clearly made sense to Phil Coppens, a crystallographer of
considerable repute, see ITC Vol. B (2nd Ed.), sect 1.2., p.10: 'The
Structure Factor'.  To quote the introduction to the section: "The
'structure factor' is the central concept in structure analysis by
diffraction methods.  Its modulus is called the 'structure  
amplitude'".


Also I did a 'Google vote' for the two terms.  'Structure  
amplitude' has
11300 hits.  'Structure factor amplitude' has only 4750.  So all  
round I

would say that 'structure amplitude' wins by a considerable margin.



Having had a quick look at the google results myself, I think that  
there

is a problem is the methodology. Google doesn't take into account
punctuation when searching. So the first search includes results  
such as
'structure. Amplitude', where the two words are in different  
sentences,
or 'structure, amplitude' where the words are part of a list. Given  
this

case, the winning margin is likely to be less.

My preference would also be for the full 'Structure factor amplitude'.
'Structure amplitude' leaves me with visions of comparing the pdb  
files

of a small single domain protein and a ribosome. Two structures having
different sizes (or amplitudes).


Cheers

-- Ian


-Original Message-
From: owner-ccp...@jiscmail.ac.uk
[mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Pavel Afonine
Sent: 11 January 2009 03:01
To: Ethan A Merritt
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] structure (factor) amplitude



On 1/10/2009 5:14 PM, Ethan A Merritt wrote:

On Saturday 10 January 2009, Bernhard Rupp wrote:


Dear All,

I am getting conflicting comments on the use of
'structure factor amplitude'
vs. just
'structure amplitude'
for |F|.



???
That's just... odd.

|F| is the amplitude of F.
But no way F is a "structure".



I agree. If F is a structure factor then |F| is a structure
factor amplitude. "structure amplitude" doesn't make much sense...
Pavel.



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 i.tic...@astex-therapeutics.com  
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




Dr. Sue A. Roberts
Biochemistry & Molecular Biophysics
University of Arizona
520 621 8171
s...@email.arizona.edu
http://www.biochem.arizona.edu/xray

Re: [ccp4bb] structure (factor) amplitude

[Andrew Purkiss-Trew]

On Mon, 2009-01-12 at 10:42 +, Ian Tickle wrote:
> I was taught 'structure amplitude' - makes perfect sense to me!  Why
> does 'structure amplitude' make any less sense than 'structure factor'?
> 
> It also clearly made sense to Phil Coppens, a crystallographer of
> considerable repute, see ITC Vol. B (2nd Ed.), sect 1.2., p.10: 'The
> Structure Factor'.  To quote the introduction to the section: "The
> 'structure factor' is the central concept in structure analysis by
> diffraction methods.  Its modulus is called the 'structure amplitude'".
> 
> Also I did a 'Google vote' for the two terms.  'Structure amplitude' has
> 11300 hits.  'Structure factor amplitude' has only 4750.  So all round I
> would say that 'structure amplitude' wins by a considerable margin.
> 

Having had a quick look at the google results myself, I think that there
is a problem is the methodology. Google doesn't take into account
punctuation when searching. So the first search includes results such as
'structure. Amplitude', where the two words are in different sentences,
or 'structure, amplitude' where the words are part of a list. Given this
case, the winning margin is likely to be less.

My preference would also be for the full 'Structure factor amplitude'.
'Structure amplitude' leaves me with visions of comparing the pdb files
of a small single domain protein and a ribosome. Two structures having
different sizes (or amplitudes).

> Cheers
> 
> -- Ian
> 
> > -Original Message-
> > From: owner-ccp...@jiscmail.ac.uk 
> > [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Pavel Afonine
> > Sent: 11 January 2009 03:01
> > To: Ethan A Merritt
> > Cc: CCP4BB@jiscmail.ac.uk
> > Subject: Re: [ccp4bb] structure (factor) amplitude
> > 
> > 
> > 
> > On 1/10/2009 5:14 PM, Ethan A Merritt wrote: 
> > 
> > On Saturday 10 January 2009, Bernhard Rupp wrote:
> >   
> > 
> > Dear All,
> > 
> > I am getting conflicting comments on the use of 
> > 'structure factor amplitude'
> > vs. just
> > 'structure amplitude'
> > for |F|.
> > 
> > 
> > 
> > ???
> > That's just... odd.
> > 
> > |F| is the amplitude of F.
> > But no way F is a "structure".
> >   
> > 
> > 
> > I agree. If F is a structure factor then |F| is a structure 
> > factor amplitude. "structure amplitude" doesn't make much sense...
> > Pavel.
> 
> 
> 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 
> i.tic...@astex-therapeutics.com 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

[ccp4bb] Postdoctoral position at the University of Liverpool

[Michael Hough]

THE UNIVERSITY OF LIVERPOOL



 SCHOOL OF BIOLOGICAL SCIENCES



POSTDOCTORAL RESEARCHER



£30,594 pa



You will join the Molecular Biophysics Group  
(www.biophysics.liv.ac.uk) to work on a BBSRC-supported project on  
structure-function-mechanism studies of copper nitrite reductases.  
The project will link crystallographic studies with fast reaction  
kinetic techniques. Our overall aim is to understand the mechanisms  
of proton coupled and conformationally coupled electron transfer  
processes in redox enzymes catalysis.  You will be responsible for  
purifying enzymes and mutants and undertake crystallographic,  
spectroscopic and mechanistic aspects of the programme.




You should have a PhD in a relevant area with experience in X-ray  
protein crystallography and practical knowledge in protein  
purification and molecular biology. The post is available for 3 years.


Job Ref: R-569018

Closing Date: 16 February 2009

For full details, or to request an application pack,visit  
www.liv.ac.uk/working/job_vacancies/


or e-mail j...@liv.ac.uk Tel 0151 794 2210 (24 hr answerphone),  
please quote Job Ref in all enquiries

Re: [ccp4bb] structure (factor) amplitude

[Alessandro Vannini]

Dear Tassos,

just to add some pepper to the conversation,
I am obliged to say that "Chichero" (as it's typed) in modern (as well  
as in old) italian would be pronounced in exactly the same way as  
greek "Kikero" ...

Does it help, or make more confusion ???

:-)

alE

PS. I am also for Structure factor amplitude. I learned it like that  
and, you know, change is bad 



***
Dr. Alessandro Vannini, PhD
Cramer lab
Gene Center, Deparment of Chemistry and Biochemistry
Ludwig-Maximilian-Universität München
Feodor-Lynen-Str. 25
81377 München
Tel. : +49-89-2180-76955


On 12 Jan 2009, at 15:15, Anastassis Perrakis wrote:

This chain reminds me of another discussion we had during dinner at  
Grenoble in the late '90s.

The topic of the argument was how to pronounce the name 'Cicero'.
Namely, my Italian friend (Gino C) was claiming it should be  
pronounced like in modern Italian, 'Chichero',
while I was claiming that since the contemporary Greeks transcribed  
it as 'Kikero' (with a k)

it should indeed sound as in modern Greek, Kikero.

My learned Dutch colleague (Mark vR) after a few minutes of this  
rather dull argument he exclaimed in the well known

Dutch diplomatic manner: 'But, who chares?'

Not that I don't care, but I would personally understand the same  
thing in both cases - and I am enjoying the argument.


A.

PS Wikipedia says: Marcus Tullius Cicero (Classical Latin pronounced  
[ˈkikeroː], usually pronounced /ˈsɪsəɹəʊ/ in English; January  
3, 106 BC – December 7, 43 BC) was a Roman statesman, lawyer,  
political theorist, philosopher, and Roman constitutionalist.


On Jan 12, 2009, at 14:48, Ian Tickle wrote:


Hi Gerard & Marc

My answer was my interpretation of Bernhard's original question "what
*is* the currently accepted name of the object whose description is
'structure factor amplitude' ?", and was based both on authoritative
precedent, i.e. ITC Vol. B, and on frequency of current usage, i.e.
Google hits.  Carroll was making the point that in logic the name  
of an
object is minimally only an arbitrary string of characters  
(preferably

pronounceable!), like the name of a variable in a program, which
minimally need have no semantic connotations whatsoever: "a rose by  
any
other name would smell as sweet".  The only requirement is that it  
must
not be ambiguous, i.e. you can't have two different objects within  
the
same context with the same name.  For example my name 'Ian'  
provides no
semantic clues as to my description (except perhaps that I'm male),  
and

causes no problems provided no other 'Ian's enter the discussion.
However alternate names for the same object are clearly allowed
(consider names of objects in different languages).

In this case I am not offering an opinion on what I think the name
*should be*, I am merely reporting on what the name *is* (however
illogical), based on precedent and usage.  However I do accept your
argument that when making up the compound name of an object, it  
should
as far as possible also be accurately descriptive in the way it  
relates
to the names of related objects, consistent with the conflicting  
needs
for abbreviation and lack of ambiguity.  You are going much further  
than

me: you are answering a different question "what *should be* the
accepted name of ... ?".  In this case you have clearly made a strong
argument, which I accept, for establishing an alternate name for this
particular object.  However one should not create new names or change
the names of objects lightly, if misunderstandings are to be avoided.
Fortunately in this case it can be done with minimal  
misunderstanding on

the part of the readers of Bernhard's textbook (though others may
disagree on that point), provided it is pointed out that there is
precedent for an alternative name for the object in question, and
perhaps a reference should be made to the original authoritative
definition.

Cheers

-- Ian


-Original Message-
From: Gerard Bricogne [mailto:g...@globalphasing.com]
Sent: 12 January 2009 12:09
To: Ian Tickle
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] structure (factor) amplitude

Dear Ian,

   My reply to this question will be less literate and less
democratic
than yours. In spite of the nice Alice quote, I remain in
favour of trying
to use compound names whose internal structure is, as much as
possible,
"isomorphic" to the composition of meanings they refer to
(even though I am
not necessarily an unconditional fanatic of OOP). Even if,
allegedly, only
God has a name for each object that completely specifies it
and even gives
it its very existence, I feel it is not unrealistic nor
immodest to do our
best to achieve this in our scientific language. If we
modelled the rigour
of scientific language on that of Lewis Carroll's, we would
be in serious
trouble (perhaps this is why scientists enjoy his humour so
much: it is

Re: [ccp4bb] structure (factor) amplitude

[Ed Pozharski]

> Also I did a 'Google vote' for the two terms.  'Structure amplitude' has
> 11300 hits.  'Structure factor amplitude' has only 4750.  So all round I
> would say that 'structure amplitude' wins by a considerable margin.


Results of another Google vote:

"Earth is flat":
55,100,000 hits
"Earth is round":
53,600,000 hits

Take that, Galileo, Columbus and Magellan!*

Of course, this post of mine is utterly irrelevant, just like all my
other posts.  Just emphasizing that majority is not always right. 

*The vote is close enough to trigger an automatic recount, but Vatican
has already declared victory and called on its opponents to concede so
that the healing process may begin.

-- 
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
--
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
--   / Lao Tse /

Re: [ccp4bb] structure (factor) amplitude

[Anastassis Perrakis]

This chain reminds me of another discussion we had during dinner at  
Grenoble in the late '90s.

The topic of the argument was how to pronounce the name 'Cicero'.
Namely, my Italian friend (Gino C) was claiming it should be  
pronounced like in modern Italian, 'Chichero',
while I was claiming that since the contemporary Greeks transcribed it  
as 'Kikero' (with a k)

it should indeed sound as in modern Greek, Kikero.

My learned Dutch colleague (Mark vR) after a few minutes of this  
rather dull argument he exclaimed in the well known

Dutch diplomatic manner: 'But, who chares?'

Not that I don't care, but I would personally understand the same  
thing in both cases - and I am enjoying the argument.


A.

PS Wikipedia says: Marcus Tullius Cicero (Classical Latin pronounced  
[ˈkikeroː], usually pronounced /ˈsɪsəɹəʊ/ in English; January  
3, 106 BC – December 7, 43 BC) was a Roman statesman, lawyer,  
political theorist, philosopher, and Roman constitutionalist.


On Jan 12, 2009, at 14:48, Ian Tickle wrote:


Hi Gerard & Marc

My answer was my interpretation of Bernhard's original question "what
*is* the currently accepted name of the object whose description is
'structure factor amplitude' ?", and was based both on authoritative
precedent, i.e. ITC Vol. B, and on frequency of current usage, i.e.
Google hits.  Carroll was making the point that in logic the name of  
an

object is minimally only an arbitrary string of characters (preferably
pronounceable!), like the name of a variable in a program, which
minimally need have no semantic connotations whatsoever: "a rose by  
any
other name would smell as sweet".  The only requirement is that it  
must

not be ambiguous, i.e. you can't have two different objects within the
same context with the same name.  For example my name 'Ian' provides  
no
semantic clues as to my description (except perhaps that I'm male),  
and

causes no problems provided no other 'Ian's enter the discussion.
However alternate names for the same object are clearly allowed
(consider names of objects in different languages).

In this case I am not offering an opinion on what I think the name
*should be*, I am merely reporting on what the name *is* (however
illogical), based on precedent and usage.  However I do accept your
argument that when making up the compound name of an object, it should
as far as possible also be accurately descriptive in the way it  
relates

to the names of related objects, consistent with the conflicting needs
for abbreviation and lack of ambiguity.  You are going much further  
than

me: you are answering a different question "what *should be* the
accepted name of ... ?".  In this case you have clearly made a strong
argument, which I accept, for establishing an alternate name for this
particular object.  However one should not create new names or change
the names of objects lightly, if misunderstandings are to be avoided.
Fortunately in this case it can be done with minimal  
misunderstanding on

the part of the readers of Bernhard's textbook (though others may
disagree on that point), provided it is pointed out that there is
precedent for an alternative name for the object in question, and
perhaps a reference should be made to the original authoritative
definition.

Cheers

-- Ian


-Original Message-
From: Gerard Bricogne [mailto:g...@globalphasing.com]
Sent: 12 January 2009 12:09
To: Ian Tickle
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] structure (factor) amplitude

Dear Ian,

My reply to this question will be less literate and less
democratic
than yours. In spite of the nice Alice quote, I remain in
favour of trying
to use compound names whose internal structure is, as much as
possible,
"isomorphic" to the composition of meanings they refer to
(even though I am
not necessarily an unconditional fanatic of OOP). Even if,
allegedly, only
God has a name for each object that completely specifies it
and even gives
it its very existence, I feel it is not unrealistic nor
immodest to do our
best to achieve this in our scientific language. If we
modelled the rigour
of scientific language on that of Lewis Carroll's, we would
be in serious
trouble (perhaps this is why scientists enjoy his humour so
much: it is
like taking off a pair of tight shoes; and it was probably
his own escape
from the rigours of mathematical logic).

In this case, the word "factor" refers to the fact that,
in the Darwin
formula for an integrated intensity, there are many factors
in a complicated
algebraic expression, and that one of them depends on the
internal structure
of the crystal. The relation to Fourier theory makes it
desirable to use as
the basic structure-dependent quantity the complex Fourier
coefficient of
the electron density, so the latter then becomes known as the
"structure
(-dependent) factor (in the Darwin formula)". Being a complex
number, it
inherits as an attribute the modulus of that complex number,
for which the
synonym "amplitude" is used - r

Re: [ccp4bb] X-Stream 2000 problem - ICING

[Santarsiero, Bernard D.]

We've been able to run months with an old Xstream 2000 system, so that
shouldn't be the problem. Unlike Frank, we haven't had problems with water
in the nitrogen from a nitrogen generator.

If Frank is correct, that it's water, then either the molecular sieves
need to be replaced, or there is ice buildup and blockage in the coldhead.
Usually blockage in the coldhead means that you can't get down in temp, or
can't maintain it within 1 degree or less. We do bring the temp up, run it
at RT over the weekend to dry things out, and then bring it down for
routine cooling.

If it's turbulence, then you don't have the warm and cold flow rates set
correctly. One thing you can see immediately, upon getting down to 100K,
is how far is the frosting plume from the tip of the nozzle. If you adjust
the flow rates, you can move that plume, caused by turbulence, closer or
further from the nozzle. It's also possible that there is something in the
nozzle that is causing turbulence no matter what the flow rates are, and
your vendor needs to look at that.

Bernie Santarsiero


On Mon, January 12, 2009 6:11 am, Frank von Delft wrote:
> Hi Mark
>
> We had a LOT of pain with icing, and it really comes down to one thing:
> water in the gN2.  And don't expect to measure some other way whether
> you have it, because your X-stream (or Cobra) is the most sensitive
> water meter there is.
>
> In our case, the symptom was the X-stream (and later Cobra) blocking up
> after between several days and several hours.  And we solved it by
> ditching the gN2 generators we were using, and organising boil-off gN2
> (much purer).
>
> The secondary effect of sample icing:  we'd see this as well if we had
> something (e.g. collimator) poking into the cold stream*:  that causes
> turbulence which draws in moisture.  Worst case you see ice flakes flick
> onto the crystal in real time;  best case you get an ice ball after a
> few minutes to hours.
>
> (* technically, the stationary phase between the cold and warm streams.)
>
> Hope that helps.
> phx
>
>
> Mark Agacan wrote:
>> Apologies for this slightly off topic question:
>>
>> I am having a great deal of trouble with my X-Stream 2000 cryostream
>> system and I wondered if other users have similar problems.
>>
>> I've replaced almost all components (new GAST compressors, helium
>> recharges, filters, etc., etc.) in the last couple of months but there
>> is almost always icing of any cryo within 10 - 20 minutes of mounting a
>> loop, and it is adversely affecting data collections.
>>
>> It appears like there is too much moisture in the cold or wam streams
>> but the tubes have been fully dried out as per Rigaku advice.
>>
>> This X-Stream is attached to a generator with inverted phi axis and and
>> i'm wondering if this could be the source of the problem, as the
>> X-Stream for another generator in the same laboratory with normal phi
>> axis does not ice up.  Can some sort of turbulence around the loop
>> caused by backdraft from the cryo hitting the inverted phi axis / camera
>> mount cause excess humidity and lead to icing on the pin, loop and
>> crystal?
>>
>> Has anyone else got this problem?  Any suggestions would be very
>> gratefully appreciated.
>>
>> Best Wishes,
>>
>> Mark
>>
>>
>> _
>> Dr Mark Agacan
>> Scientific Officer,
>> Division of Biological Chemistry
>> and Drug Discovery,
>> Wellcome Trust Biocentre,
>> College of Life Sciences,
>> Dow St.,
>> University of Dundee,
>> Dundee, DD1 5EH
>> Tel: +44 1382 388751
>> Fax: +44 1382 345764
>> _
>> The University of Dundee is a registered Scottish charity, No: SC015096
>>
>

Re: [ccp4bb] structure (factor) amplitude

[Ian Tickle]

Hi Gerard & Marc

My answer was my interpretation of Bernhard's original question "what
*is* the currently accepted name of the object whose description is
'structure factor amplitude' ?", and was based both on authoritative
precedent, i.e. ITC Vol. B, and on frequency of current usage, i.e.
Google hits.  Carroll was making the point that in logic the name of an
object is minimally only an arbitrary string of characters (preferably
pronounceable!), like the name of a variable in a program, which
minimally need have no semantic connotations whatsoever: "a rose by any
other name would smell as sweet".  The only requirement is that it must
not be ambiguous, i.e. you can't have two different objects within the
same context with the same name.  For example my name 'Ian' provides no
semantic clues as to my description (except perhaps that I'm male), and
causes no problems provided no other 'Ian's enter the discussion.
However alternate names for the same object are clearly allowed
(consider names of objects in different languages).

In this case I am not offering an opinion on what I think the name
*should be*, I am merely reporting on what the name *is* (however
illogical), based on precedent and usage.  However I do accept your
argument that when making up the compound name of an object, it should
as far as possible also be accurately descriptive in the way it relates
to the names of related objects, consistent with the conflicting needs
for abbreviation and lack of ambiguity.  You are going much further than
me: you are answering a different question "what *should be* the
accepted name of ... ?".  In this case you have clearly made a strong
argument, which I accept, for establishing an alternate name for this
particular object.  However one should not create new names or change
the names of objects lightly, if misunderstandings are to be avoided.
Fortunately in this case it can be done with minimal misunderstanding on
the part of the readers of Bernhard's textbook (though others may
disagree on that point), provided it is pointed out that there is
precedent for an alternative name for the object in question, and
perhaps a reference should be made to the original authoritative
definition.

Cheers

-- Ian

> -Original Message-
> From: Gerard Bricogne [mailto:g...@globalphasing.com] 
> Sent: 12 January 2009 12:09
> To: Ian Tickle
> Cc: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] structure (factor) amplitude
> 
> Dear Ian,
> 
>  My reply to this question will be less literate and less 
> democratic
> than yours. In spite of the nice Alice quote, I remain in 
> favour of trying
> to use compound names whose internal structure is, as much as 
> possible,
> "isomorphic" to the composition of meanings they refer to 
> (even though I am
> not necessarily an unconditional fanatic of OOP). Even if, 
> allegedly, only
> God has a name for each object that completely specifies it 
> and even gives
> it its very existence, I feel it is not unrealistic nor 
> immodest to do our
> best to achieve this in our scientific language. If we 
> modelled the rigour
> of scientific language on that of Lewis Carroll's, we would 
> be in serious
> trouble (perhaps this is why scientists enjoy his humour so 
> much: it is
> like taking off a pair of tight shoes; and it was probably 
> his own escape 
> from the rigours of mathematical logic).
> 
>  In this case, the word "factor" refers to the fact that, 
> in the Darwin
> formula for an integrated intensity, there are many factors 
> in a complicated
> algebraic expression, and that one of them depends on the 
> internal structure
> of the crystal. The relation to Fourier theory makes it 
> desirable to use as
> the basic structure-dependent quantity the complex Fourier 
> coefficient of
> the electron density, so the latter then becomes known as the 
> "structure
> (-dependent) factor (in the Darwin formula)". Being a complex 
> number, it
> inherits as an attribute the modulus of that complex number, 
> for which the
> synonym "amplitude" is used - regrettably, but possibly 
> because the word
> "modulus" was already widely used, e.g. in the theory of elasticity. 
> 
>  Therefore the expression "structure factor amplitude" 
> can be parsed as
> being "the amplitude (a.k.a. modulus) of a complex number 
> which is involved
> in the structure-dependent factor in the Darwin formula". 
> Along with Dirk
> Kostrewa I vote for retaining the full-length expression, as 
> the abbreviated
> one makes one think that a structure has an amplitude ... .
> 
>  Abbreviations can be great, but they can also result in 
> a substantial
> loss of intelligibility. Look at the transition to "Brazilian 
> spelling" in
> Portuguese, whereby "optimo" is abbreviated to "otimo". A 
> non-Portuguese
> speaker (even an English-only speaker!) can understand the 
> word from its
> first spelling because the Latin derivation is clear; but 
> this is no longer
> the case for the abbreviate

Re: [ccp4bb] structure (factor) amplitude

[Marc SCHILTZ]

Ian Tickle wrote:

I think there's a confusion here between the name of an object (what you
call it) and its description (i.e. its properties).  The name of the
object is "structure amplitude" and it's description is "amplitude of
the structure factor", or if you prefer the shortened form "structure
factor amplitude". 



But one does not name the modulus of a complex number a "complex 
modulus"; one does not name the amplitude of a molecular vibration a 
"molecular amplitude"; and one does not name the trace of a rotation 
matrix a "rotation trace".




Mal nommer les choses, c'est ajouter au malheur des hommes. A.Camus.


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

Re: [ccp4bb] X-Stream 2000 problem - ICING

[Johan P. Turkenburg]

Hi,

If you have ice on the crystal (loop) but no blockages of the cryostream 
itself (and this seems to be what you're saying), it is unlikely to be a 
problem with the LN2 (although I only have experience with Oxford 
Crystreams, but I imagine this also applies to X-streams).


Our main problems are turbulence (collimator poking into the gas 
stream(s) or gas 'bouncing' back from something just beyond the crystal 
- moving things even a little may help here) and drafts due to 
'powerful' air-conditioning.


As you state that one of your setups is affected and not the other, it 
may well be the case that an air conditioning vent is blowing onto your 
setup, and disturbing the gas streams. We resorted to hanging plastic 
sheeting around two sides of our set-up and this made a vast difference.


HTH,

Johan

Mark Agacan wrote:
Apologies for this slightly off topic question:  

I am having a great deal of trouble with my X-Stream 2000 cryostream system and I wondered if other users have similar problems.  

I've replaced almost all components (new GAST compressors, helium recharges, filters, etc., etc.) in the last couple of months but there is almost always icing of any cryo within 10 - 20 minutes of mounting a loop, and it is adversely affecting data collections.  

It appears like there is too much moisture in the cold or wam streams but the tubes have been fully dried out as per Rigaku advice.  

This X-Stream is attached to a generator with inverted phi axis and and i'm wondering if this could be the source of the problem, as the X-Stream for another generator in the same laboratory with normal phi axis does not ice up.  Can some sort of turbulence around the loop caused by backdraft from the cryo hitting the inverted phi axis / camera mount cause excess humidity and lead to icing on the pin, loop and crystal?  


Has anyone else got this problem?  Any suggestions would be very gratefully 
appreciated.

Best Wishes,

Mark


_
Dr Mark Agacan
Scientific Officer,
Division of Biological Chemistry 
and Drug Discovery,

Wellcome Trust Biocentre,
College of Life Sciences,
Dow St., 
University of Dundee,

Dundee, DD1 5EH
Tel: +44 1382 388751
Fax: +44 1382 345764
_
The University of Dundee is a registered Scottish charity, No: SC015096





--
+
Dr. Johan P. Turkenburg X-ray facilities manager
York Structural Biology Laboratory  
University of York  Phone (+) 44 1904 328251
York YO10 5DD   UK  Fax   (+) 44 1904 328266
+

Re: [ccp4bb] X-Stream 2000 problem - ICING

[Frank von Delft]

Hi Mark

We had a LOT of pain with icing, and it really comes down to one thing:  
water in the gN2.  And don't expect to measure some other way whether 
you have it, because your X-stream (or Cobra) is the most sensitive 
water meter there is. 

In our case, the symptom was the X-stream (and later Cobra) blocking up 
after between several days and several hours.  And we solved it by 
ditching the gN2 generators we were using, and organising boil-off gN2 
(much purer).


The secondary effect of sample icing:  we'd see this as well if we had 
something (e.g. collimator) poking into the cold stream*:  that causes 
turbulence which draws in moisture.  Worst case you see ice flakes flick 
onto the crystal in real time;  best case you get an ice ball after a 
few minutes to hours. 


(* technically, the stationary phase between the cold and warm streams.)

Hope that helps.
phx


Mark Agacan wrote:
Apologies for this slightly off topic question:  

I am having a great deal of trouble with my X-Stream 2000 cryostream system and I wondered if other users have similar problems.  

I've replaced almost all components (new GAST compressors, helium recharges, filters, etc., etc.) in the last couple of months but there is almost always icing of any cryo within 10 - 20 minutes of mounting a loop, and it is adversely affecting data collections.  

It appears like there is too much moisture in the cold or wam streams but the tubes have been fully dried out as per Rigaku advice.  

This X-Stream is attached to a generator with inverted phi axis and and i'm wondering if this could be the source of the problem, as the X-Stream for another generator in the same laboratory with normal phi axis does not ice up.  Can some sort of turbulence around the loop caused by backdraft from the cryo hitting the inverted phi axis / camera mount cause excess humidity and lead to icing on the pin, loop and crystal?  


Has anyone else got this problem?  Any suggestions would be very gratefully 
appreciated.

Best Wishes,

Mark


_
Dr Mark Agacan
Scientific Officer,
Division of Biological Chemistry 
and Drug Discovery,

Wellcome Trust Biocentre,
College of Life Sciences,
Dow St., 
University of Dundee,

Dundee, DD1 5EH
Tel: +44 1382 388751
Fax: +44 1382 345764
_
The University of Dundee is a registered Scottish charity, No: SC015096
  

Re: [ccp4bb] structure (factor) amplitude

[Gerard Bricogne]

Dear Ian,

 My reply to this question will be less literate and less democratic
than yours. In spite of the nice Alice quote, I remain in favour of trying
to use compound names whose internal structure is, as much as possible,
"isomorphic" to the composition of meanings they refer to (even though I am
not necessarily an unconditional fanatic of OOP). Even if, allegedly, only
God has a name for each object that completely specifies it and even gives
it its very existence, I feel it is not unrealistic nor immodest to do our
best to achieve this in our scientific language. If we modelled the rigour
of scientific language on that of Lewis Carroll's, we would be in serious
trouble (perhaps this is why scientists enjoy his humour so much: it is
like taking off a pair of tight shoes; and it was probably his own escape 
from the rigours of mathematical logic).

 In this case, the word "factor" refers to the fact that, in the Darwin
formula for an integrated intensity, there are many factors in a complicated
algebraic expression, and that one of them depends on the internal structure
of the crystal. The relation to Fourier theory makes it desirable to use as
the basic structure-dependent quantity the complex Fourier coefficient of
the electron density, so the latter then becomes known as the "structure
(-dependent) factor (in the Darwin formula)". Being a complex number, it
inherits as an attribute the modulus of that complex number, for which the
synonym "amplitude" is used - regrettably, but possibly because the word
"modulus" was already widely used, e.g. in the theory of elasticity. 

 Therefore the expression "structure factor amplitude" can be parsed as
being "the amplitude (a.k.a. modulus) of a complex number which is involved
in the structure-dependent factor in the Darwin formula". Along with Dirk
Kostrewa I vote for retaining the full-length expression, as the abbreviated
one makes one think that a structure has an amplitude ... .

 Abbreviations can be great, but they can also result in a substantial
loss of intelligibility. Look at the transition to "Brazilian spelling" in
Portuguese, whereby "optimo" is abbreviated to "otimo". A non-Portuguese
speaker (even an English-only speaker!) can understand the word from its
first spelling because the Latin derivation is clear; but this is no longer
the case for the abbreviated one, unless one also remembers what it is an
abbreviation of. Similarly, "structure amplitude" does not tell you that
there is a complex number called the structure factor, of which one is
considering the amplitude/modulus.

 Sorry for this long message: as the question originated from Bernhard,
who is in the process of writing a textbook, I think it is important that
points of terminology like this one be given careful consideration and a
satisfactory conclusion; so I hope that many other people will give some
attention to this thread (even if they disagree with me!). 


 With best wishes,
 
  Gerard.


--
On Mon, Jan 12, 2009 at 11:09:34AM -, Ian Tickle wrote:
> I think there's a confusion here between the name of an object (what you
> call it) and its description (i.e. its properties).  The name of the
> object is "structure amplitude" and it's description is "amplitude of
> the structure factor", or if you prefer the shortened form "structure
> factor amplitude".  This distinction was of course carried to absurdity
> in "Alice through the Looking Glass":
> 
> "It's long." said the Knight, "but it's very, very beautiful. Everybody
> that hears me sing it - either it brings tears to their eyes, or else -"
> "Or else what?" said Alice, for the Knight had made a sudden pause.
> "Or else it doesn't, you know. The name of the song is called 'Haddocks'
> Eyes.'"
> "Oh, that's the name of the song, is it?" Alice said, trying to feel
> interested.
> "No, you don't understand," the Knight said, looking a little vexed.
> "That's what the name is called. The name really is 'The Aged, Aged
> Man.'"
> "Then I ought to have said 'That's what the song is called'?" Alice
> corrected herself.
> "No you oughtn't: that's another thing. The song is called 'Ways and
> Means' but that's only what it's called, you know!"
> "Well, what is the song then?" said Alice, who was by this time
> completely bewildered.
> "I was coming to that," the Knight said. "The song really is 'A-sitting
> On a Gate': and the tune's my own invention."
> 
> Cheers
> 
> -- Ian
> 
> > -Original Message-
> > From: owner-ccp...@jiscmail.ac.uk 
> > [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Dirk Kostrewa
> > Sent: 12 January 2009 10:52
> > To: CCP4BB
> > Subject: Re: [ccp4bb] structure (factor) amplitude
> > 
> > ... despite these informations, I still prefer "structure factor  
> > amplitude", because it is the amplitude of the "structure factor" ...
> > 
> > Best regards,
> > 
> > Dirk.
> > 
> > Am 12.01.2009 um 11:42 schrieb Ian Tickle:
> > 
> > > I was taught 'structure amplitu

Re: [ccp4bb] structure (factor) amplitude

[Dirk Kostrewa]

Dear Ian,

many thanks for this clarification - I have to think about this,  
though ;-)


Best regards,

Dirk.

Am 12.01.2009 um 12:09 schrieb Ian Tickle:

I think there's a confusion here between the name of an object (what  
you

call it) and its description (i.e. its properties).  The name of the
object is "structure amplitude" and it's description is "amplitude of
the structure factor", or if you prefer the shortened form "structure
factor amplitude".  This distinction was of course carried to  
absurdity

in "Alice through the Looking Glass":

"It's long." said the Knight, "but it's very, very beautiful.  
Everybody
that hears me sing it - either it brings tears to their eyes, or  
else -"

"Or else what?" said Alice, for the Knight had made a sudden pause.
"Or else it doesn't, you know. The name of the song is called  
'Haddocks'

Eyes.'"
"Oh, that's the name of the song, is it?" Alice said, trying to feel
interested.
"No, you don't understand," the Knight said, looking a little vexed.
"That's what the name is called. The name really is 'The Aged, Aged
Man.'"
"Then I ought to have said 'That's what the song is called'?" Alice
corrected herself.
"No you oughtn't: that's another thing. The song is called 'Ways and
Means' but that's only what it's called, you know!"
"Well, what is the song then?" said Alice, who was by this time
completely bewildered.
"I was coming to that," the Knight said. "The song really is 'A- 
sitting

On a Gate': and the tune's my own invention."

Cheers

-- Ian


-Original Message-
From: owner-ccp...@jiscmail.ac.uk
[mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Dirk Kostrewa
Sent: 12 January 2009 10:52
To: CCP4BB
Subject: Re: [ccp4bb] structure (factor) amplitude

... despite these informations, I still prefer "structure factor
amplitude", because it is the amplitude of the "structure factor" ...

Best regards,

Dirk.

Am 12.01.2009 um 11:42 schrieb Ian Tickle:


I was taught 'structure amplitude' - makes perfect sense to me!  Why
does 'structure amplitude' make any less sense than 'structure
factor'?

It also clearly made sense to Phil Coppens, a crystallographer of
considerable repute, see ITC Vol. B (2nd Ed.), sect 1.2., p.10: 'The
Structure Factor'.  To quote the introduction to the section: "The
'structure factor' is the central concept in structure analysis by
diffraction methods.  Its modulus is called the 'structure
amplitude'".

Also I did a 'Google vote' for the two terms.  'Structure

amplitude'

has
11300 hits.  'Structure factor amplitude' has only 4750.  So all
round I
would say that 'structure amplitude' wins by a considerable margin.

Cheers

-- Ian


-Original Message-
From: owner-ccp...@jiscmail.ac.uk
[mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Pavel Afonine
Sent: 11 January 2009 03:01
To: Ethan A Merritt
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] structure (factor) amplitude



On 1/10/2009 5:14 PM, Ethan A Merritt wrote:

On Saturday 10 January 2009, Bernhard Rupp wrote:


Dear All,

I am getting conflicting comments on the use of
'structure factor amplitude'
vs. just
'structure amplitude'
for |F|.



???
That's just... odd.

|F| is the amplitude of F.
But no way F is a "structure".



I agree. If F is a structure factor then |F| is a structure
factor amplitude. "structure amplitude" doesn't make much sense...
Pavel.



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Re: [ccp4bb] structure (factor) amplitude

[Ian Tickle]

I think there's a confusion here between the name of an object (what you
call it) and its description (i.e. its properties).  The name of the
object is "structure amplitude" and it's description is "amplitude of
the structure factor", or if you prefer the shortened form "structure
factor amplitude".  This distinction was of course carried to absurdity
in "Alice through the Looking Glass":

"It's long." said the Knight, "but it's very, very beautiful. Everybody
that hears me sing it - either it brings tears to their eyes, or else -"
"Or else what?" said Alice, for the Knight had made a sudden pause.
"Or else it doesn't, you know. The name of the song is called 'Haddocks'
Eyes.'"
"Oh, that's the name of the song, is it?" Alice said, trying to feel
interested.
"No, you don't understand," the Knight said, looking a little vexed.
"That's what the name is called. The name really is 'The Aged, Aged
Man.'"
"Then I ought to have said 'That's what the song is called'?" Alice
corrected herself.
"No you oughtn't: that's another thing. The song is called 'Ways and
Means' but that's only what it's called, you know!"
"Well, what is the song then?" said Alice, who was by this time
completely bewildered.
"I was coming to that," the Knight said. "The song really is 'A-sitting
On a Gate': and the tune's my own invention."

Cheers

-- Ian

> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk 
> [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Dirk Kostrewa
> Sent: 12 January 2009 10:52
> To: CCP4BB
> Subject: Re: [ccp4bb] structure (factor) amplitude
> 
> ... despite these informations, I still prefer "structure factor  
> amplitude", because it is the amplitude of the "structure factor" ...
> 
> Best regards,
> 
> Dirk.
> 
> Am 12.01.2009 um 11:42 schrieb Ian Tickle:
> 
> > I was taught 'structure amplitude' - makes perfect sense to me!  Why
> > does 'structure amplitude' make any less sense than 'structure  
> > factor'?
> >
> > It also clearly made sense to Phil Coppens, a crystallographer of
> > considerable repute, see ITC Vol. B (2nd Ed.), sect 1.2., p.10: 'The
> > Structure Factor'.  To quote the introduction to the section: "The
> > 'structure factor' is the central concept in structure analysis by
> > diffraction methods.  Its modulus is called the 'structure  
> > amplitude'".
> >
> > Also I did a 'Google vote' for the two terms.  'Structure 
> amplitude'  
> > has
> > 11300 hits.  'Structure factor amplitude' has only 4750.  So all  
> > round I
> > would say that 'structure amplitude' wins by a considerable margin.
> >
> > Cheers
> >
> > -- Ian
> >
> >> -Original Message-
> >> From: owner-ccp...@jiscmail.ac.uk
> >> [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Pavel Afonine
> >> Sent: 11 January 2009 03:01
> >> To: Ethan A Merritt
> >> Cc: CCP4BB@jiscmail.ac.uk
> >> Subject: Re: [ccp4bb] structure (factor) amplitude
> >>
> >>
> >>
> >> On 1/10/2009 5:14 PM, Ethan A Merritt wrote:
> >>
> >>On Saturday 10 January 2009, Bernhard Rupp wrote:
> >>
> >>
> >>Dear All,
> >>
> >>I am getting conflicting comments on the use of
> >>'structure factor amplitude'
> >>vs. just
> >>'structure amplitude'
> >>for |F|.
> >>
> >>
> >>
> >>???
> >>That's just... odd.
> >>
> >>|F| is the amplitude of F.
> >>But no way F is a "structure".
> >>
> >>
> >>
> >> I agree. If F is a structure factor then |F| is a structure
> >> factor amplitude. "structure amplitude" doesn't make much sense...
> >> Pavel.
> >
> >
> > 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 i.tic...@astex-therapeutics.com  
> > 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  
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> > Therapeutics Ltd only

[ccp4bb] X-Stream 2000 problem - ICING

[Mark Agacan]

Apologies for this slightly off topic question:  

I am having a great deal of trouble with my X-Stream 2000 cryostream system and 
I wondered if other users have similar problems.  

I've replaced almost all components (new GAST compressors, helium recharges, 
filters, etc., etc.) in the last couple of months but there is almost always 
icing of any cryo within 10 - 20 minutes of mounting a loop, and it is 
adversely affecting data collections.  

It appears like there is too much moisture in the cold or wam streams but the 
tubes have been fully dried out as per Rigaku advice.  

This X-Stream is attached to a generator with inverted phi axis and and i'm 
wondering if this could be the source of the problem, as the X-Stream for 
another generator in the same laboratory with normal phi axis does not ice up.  
Can some sort of turbulence around the loop caused by backdraft from the cryo 
hitting the inverted phi axis / camera mount cause excess humidity and lead to 
icing on the pin, loop and crystal?  

Has anyone else got this problem?  Any suggestions would be very gratefully 
appreciated.

Best Wishes,

Mark


_
Dr Mark Agacan
Scientific Officer,
Division of Biological Chemistry 
and Drug Discovery,
Wellcome Trust Biocentre,
College of Life Sciences,
Dow St., 
University of Dundee,
Dundee, DD1 5EH
Tel: +44 1382 388751
Fax: +44 1382 345764
_
The University of Dundee is a registered Scottish charity, No: SC015096

Re: [ccp4bb] structure (factor) amplitude

[Dirk Kostrewa]

... despite these informations, I still prefer "structure factor  
amplitude", because it is the amplitude of the "structure factor" ...


Best regards,

Dirk.

Am 12.01.2009 um 11:42 schrieb Ian Tickle:


I was taught 'structure amplitude' - makes perfect sense to me!  Why
does 'structure amplitude' make any less sense than 'structure  
factor'?


It also clearly made sense to Phil Coppens, a crystallographer of
considerable repute, see ITC Vol. B (2nd Ed.), sect 1.2., p.10: 'The
Structure Factor'.  To quote the introduction to the section: "The
'structure factor' is the central concept in structure analysis by
diffraction methods.  Its modulus is called the 'structure  
amplitude'".


Also I did a 'Google vote' for the two terms.  'Structure amplitude'  
has
11300 hits.  'Structure factor amplitude' has only 4750.  So all  
round I

would say that 'structure amplitude' wins by a considerable margin.

Cheers

-- Ian


-Original Message-
From: owner-ccp...@jiscmail.ac.uk
[mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Pavel Afonine
Sent: 11 January 2009 03:01
To: Ethan A Merritt
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] structure (factor) amplitude



On 1/10/2009 5:14 PM, Ethan A Merritt wrote:

On Saturday 10 January 2009, Bernhard Rupp wrote:


Dear All,

I am getting conflicting comments on the use of
'structure factor amplitude'
vs. just
'structure amplitude'
for |F|.



???
That's just... odd.

|F| is the amplitude of F.
But no way F is a "structure".



I agree. If F is a structure factor then |F| is a structure
factor amplitude. "structure amplitude" doesn't make much sense...
Pavel.



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 i.tic...@astex-therapeutics.com  
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  
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Therapeutics domain.  Unless expressly stated, opinions in this  
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***
Dirk Kostrewa
Gene Center, A 5.07
Ludwig-Maximilians-University
Feodor-Lynen-Str. 25
81377 Munich
Germany
Phone:  +49-89-2180-76845
Fax:+49-89-2180-76999
E-mail: kostr...@lmb.uni-muenchen.de
***

Re: [ccp4bb] structure (factor) amplitude

[Ian Tickle]

I was taught 'structure amplitude' - makes perfect sense to me!  Why
does 'structure amplitude' make any less sense than 'structure factor'?

It also clearly made sense to Phil Coppens, a crystallographer of
considerable repute, see ITC Vol. B (2nd Ed.), sect 1.2., p.10: 'The
Structure Factor'.  To quote the introduction to the section: "The
'structure factor' is the central concept in structure analysis by
diffraction methods.  Its modulus is called the 'structure amplitude'".

Also I did a 'Google vote' for the two terms.  'Structure amplitude' has
11300 hits.  'Structure factor amplitude' has only 4750.  So all round I
would say that 'structure amplitude' wins by a considerable margin.

Cheers

-- Ian

> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk 
> [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Pavel Afonine
> Sent: 11 January 2009 03:01
> To: Ethan A Merritt
> Cc: CCP4BB@jiscmail.ac.uk
> Subject: Re: [ccp4bb] structure (factor) amplitude
> 
> 
> 
> On 1/10/2009 5:14 PM, Ethan A Merritt wrote: 
> 
>   On Saturday 10 January 2009, Bernhard Rupp wrote:
> 
> 
>   Dear All,
>   
>   I am getting conflicting comments on the use of 
>   'structure factor amplitude'
>   vs. just
>   'structure amplitude'
>   for |F|.
>   
> 
>   
>   ???
>   That's just... odd.
>   
>   |F| is the amplitude of F.
>   But no way F is a "structure".
> 
> 
> 
> I agree. If F is a structure factor then |F| is a structure 
> factor amplitude. "structure amplitude" doesn't make much sense...
> Pavel.


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 
i.tic...@astex-therapeutics.com 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