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 -0000, Ian Tickle wrote:
> I think there's a confusion here between the name of an object (what you
> call it) and its description (i.e. its properties). The name of the
> object is "structure amplitude" and it's description is "amplitude of
> the structure factor", or if you prefer the shortened form "structure
> factor amplitude". This distinction was of course carried to absurdity
> in "Alice through the Looking Glass":
>
> "It's long." said the Knight, "but it's very, very beautiful. Everybody
> that hears me sing it - either it brings tears to their eyes, or else -"
> "Or else what?" said Alice, for the Knight had made a sudden pause.
> "Or else it doesn't, you know. The name of the song is called 'Haddocks'
> Eyes.'"
> "Oh, that's the name of the song, is it?" Alice said, trying to feel
> interested.
> "No, you don't understand," the Knight said, looking a little vexed.
> "That's what the name is called. The name really is 'The Aged, Aged
> Man.'"
> "Then I ought to have said 'That's what the song is called'?" Alice
> corrected herself.
> "No you oughtn't: that's another thing. The song is called 'Ways and
> Means' but that's only what it's called, you know!"
> "Well, what is the song then?" said Alice, who was by this time
> completely bewildered.
> "I was coming to that," the Knight said. "The song really is 'A-sitting
> On a Gate': and the tune's my own invention."
>
> Cheers
>
> -- Ian
>
> > -----Original Message-----
> > From: [log in to unmask]
> > [mailto:[log in to unmask]] 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: [log in to unmask]
> > >> [mailto:[log in to unmask]] On Behalf Of Pavel Afonine
> > >> Sent: 11 January 2009 03:01
> > >> To: Ethan A Merritt
> > >> Cc: [log in to unmask]
> > >> Subject: Re: [ccp4bb] structure (factor) amplitude
> > >>
> > >>
> > >>
> > >> On 1/10/2009 5:14 PM, Ethan A Merritt wrote:
> > >>
> > >> On Saturday 10 January 2009, Bernhard Rupp wrote:
> > >>
> > >>
> > >> Dear All,
> > >>
> > >> I am getting conflicting comments on the use of
> > >> 'structure factor amplitude'
> > >> vs. just
> > >> 'structure amplitude'
> > >> for |F|.
> > >>
> > >>
> > >>
> > >> ???
> > >> That's just... odd.
> > >>
> > >> |F| is the amplitude of F.
> > >> But no way F is a "structure".
> > >>
> > >>
> > >>
> > >> I agree. If F is a structure factor then |F| is a structure
> > >> factor amplitude. "structure amplitude" doesn't make much sense...
> > >> Pavel.
> > >
> > >
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> > *******************************************************
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> 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.
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