Re: [ccp4bb] structure (factor) amplitude
rnhard'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: ccp...@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). Even20if, >> 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 wor d >> "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 "
Re: [ccp4bb] structure (factor) amplitude
> -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 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
Re: [ccp4bb] structure (factor) amplitude
- 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
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
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] structure (factor) amplitude
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 * * * === * 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
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 * * * === * 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
> 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
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] structure (factor) amplitude
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
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
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 > >>>> > >
Re: [ccp4bb] structure (factor) amplitude
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 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 Therapeu
Re: [ccp4bb] structure (factor) amplitude
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 mak
Re: [ccp4bb] structure (factor) amplitude
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 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
Re: [ccp4bb] structure (factor) amplitude
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
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
[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
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
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> [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 <mailto: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 <mailto: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
Re: [ccp4bb] structure (factor) amplitude
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 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
Re: [ccp4bb] structure (factor) amplitude
> > 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
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!"
Re: [ccp4bb] structure (factor) amplitude
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
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
Re: [ccp4bb] structure (factor) amplitude
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.
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 /
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 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
Re: [ccp4bb] structure (factor) amplitude
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
Re: [ccp4bb] structure (factor) amplitude
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] 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 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
Re: [ccp4bb] structure (factor) amplitude
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. 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 shoul
Re: [ccp4bb] structure (factor) amplitude
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 >
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 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 *** 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
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
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.
Re: [ccp4bb] structure (factor) amplitude
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". -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle 98195-7742
[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
