Re: [ccp4bb]: ab initio

[<gb10@globalphasing.com>]

***  For details on how to be removed from this list visit the  ***
***          CCP4 home page http://www.ccp4.ac.uk         ***

Dear Manfred,

     I am not sure that I would agree with you about surrendering the use of 
'ab initio' and 'de novo' to organic chemists, theoretical or practical, 
however peruasive they might be about their historical prerogatives.

     The term 'ab initio', I would think, came into use with direct methods, 
on a consensual besis which might be difficult to trace but which, I feel is 
very real. It had the meaning which George Sheldrick write down, partly at 
least in response to the same misuse which I had objected to in the mid-90's. 
The risk of confusion with 'ab initio' quantum mechanical computations does 
not really exist, and I feel that this term should be kept with its undiluted 
meaning of solving a light-atom structure from amplitudes only, without 
anomalous differences. I did acknowledge in my previous message that this 
definition might in the future become obsolete and purely/uselessly academic, 
but until this has actually happened we should retain this original meaning.

     The term 'de novo' has similarly been used in a consistent manner to 
designate the difference between experimental (hence objective) phasing and 
structure solution by molecular replacement. It is a very practical, sensible 
distinction which should be made by means of a precise expression, so I see 
no reason to abandon it as 'misguided and misunderstood Latin': it is neither. 

     What should be discouraged is the misuse of one for the other, resulting 
(although not in everyone) in short-lived excitement about implied claims. 
Readers may consult a series of papers in Acta A50 (1994) and A51 (1995) with 
general title "The ab initio crystal structure solution of proteins by direct 
methods", and judge for themselves whether the contents match the expectations 
which such a title elicited on first reading. My own conclusion had been that 
more rigour should be exercised in the use of this hallowed expression, hence 
my remarks at the time.

     
     With best wishes,

          Gerard.

--
Original message from Manfred Buehner:
> 
> ***  For details on how to be removed from this list visit the  ***
> ***          CCP4 home page http://www.ccp4.ac.uk         ***
> 
> Salve communitas!
> 
> It's a nice debate about "ab initio", confusing, amusing!
> 
> A) Language:
>    "ab initio" literally means "from the beginning"
>      (which is as trivial as unnecessary to mention,
>      except in Wonderland) and logically means "from
>      first principles".
>    "de novo" literally means "from new" (which is as
>      trivial as unnecessary to mention in science) and
>      logically means "from scratch" or "from basic
>      building blocks".
> 
> B) History:
>    "ab initio" is a technical term used for a long time
>      by theoretical (organic) chemists, meaning calculation
>      of molecular properties from wave functions and some
>      operators I personally don't know much about, without
>      using practical "chemical" knowledge.
>    "de novo" is a technical term used for a long time by
>      practical organic chemists for synthesis from very
>      basic building blocks not structurally related to the
>      final product (similar to "total synthesis").
> 
> C) Proposal:
>    Xtallographers better leave those terms alone, i.e.
>    leave them to their "inventors", the chemists, who had
>    given them a "local" precise meaning.
> 
>    If we need to express certain characteristics of some
>    ways to structure solution we might as well call them by
>    their proper crystallographic names instead of pompous-
>    ing our texts by misguided and misunderstood Latin.
>    After all, crystallography grew up long after Latin had
>    ceased to be the lingua franca of intellectual life.
>    The first edition of the International Tables were not
>    the "Tabulae Internationales", but the "Internationale
>    Tabellen".
> 
> ROMA LOCUTA, CASA FINITA
> 
> Valete,
>         Manfred
> ----------------------------------------------------------
>  Dr. Manfred Buehner             Phone:  +49-931-888-4100
>  Physiologische Chemie           FAX:    +49-931-888-4150
>  Theodor-Boveri-Institut fuer Biowissenschaften
>  Biozentrum der Universitaet Wuerzburg
>  Am Hubland,  D-97074 WUERZBURG,  Germany
>  Email:  buehner@biozentrum.uni-wuerzburg.de
> ----------------------------------------------------------
> 
-- 

     ===============================================================
     *                                                             *
     * Gerard Bricogne                     gb10@GlobalPhasing.com  *
     *                                                             *
     * Global Phasing Ltd.                                         *
     * Sheraton House, Castle Park         Tel: +44-(0)1223-353033 *
     * Cambridge CB3 0AX, UK               Fax: +44-(0)1223-366889 *
     *                                                             *
     ===============================================================