Re: [ccp4bb] [g...@globalphasing.com: [ccp4bb] An error in the IUCr Online Dictionary of Crystallography] (fwd)

2020-03-11 Thread Gerard Bricogne 
Dear all,

 I don't quite know what to say about the direction in which the initial
topic is getting derailed ... .

 The substance of it is that an official (IUCr) online definition of a
statistic very much relied upon contained both a mathematical error and an
erroneous verbal description, and that this was promptly corrected through
an immediate mobilisation of good will (thank you Randy and Brian).

 Why not leave it at that?


 With best wishes,

  Gerard.

--
On Wed, Mar 11, 2020 at 04:53:25PM +, Eleanor Dodson wrote:
> Am I missing something? He? She? It? Are they now interchangeable?
> 
> On Wed, 11 Mar 2020 at 16:15, Tim Gruene  wrote:
> 
> > Dear Gerard,
> >
> > you are wrong. 'he'  in this context has as much information as 'someone'
> > and
> > 'person'. It does not refer to the sex of the person spoken about.
> >
> > Best regards,
> > Tim
> >
> > On Wednesday, March 11, 2020 4:44:47 PM CET Gerard DVD Kleywegt wrote:
> > > >>>   Sorry to have taken this matter up in such a visible manner: I
> > > >>>   noticed
> > > >>>
> > > >>> this very wrong formula in someone's paper, and that person then
> > told me
> > > >>> where he had found it. Having landed on that page, I didn't know
> > where
> > > >>> to go
> > > For the students:
> > >
> > > "someone" = systematic absence of information = 0 bits
> > > "person" = systematic absence of information = 0 bits
> > > "he" = 1 bit of information!
> > >
> > > --The other Gerard (1 bit of information!)
> > >
> > > **
> > > Gerard J. Kleywegt
> > >
> > >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.
> > > **
> > > Little known gastromathematical curiosity: let "z" be the
> > > radius and "a" the thickness of a pizza. Then the volume
> > >  of that pizza is equal to pi*z*z*a !
> > > **
> > >
> > > 
> > >
> > > To unsubscribe from the CCP4BB list, click the following link:
> > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
> >
> > --
> > --
> > Tim Gruene
> > Head of the Centre for X-ray Structure Analysis
> > Faculty of Chemistry
> > University of Vienna
> >
> > Phone: +43-1-4277-70202
> >
> > GPG Key ID = A46BEE1A
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
> >
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1



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Re: [ccp4bb] [g...@globalphasing.com: [ccp4bb] An error in the IUCr Online Dictionary of Crystallography] (fwd)

2020-03-11 Thread Rasmus Fogh 

Dear Eleanor,

In the English I (and Gerard) learned at school, 'he' was (also) the 
generic way to refer to an unknown person. In the English of the future, 
the use of 'he' may well be discouraged altogether. Meanwhile the top 
generic pronoun is currently 'they'.


So, who knows how you are supposed to interpret that word in a BB 
message in 2020??


;-)

Rasmus Fogh

On 11/03/2020 16:53, Eleanor Dodson wrote:

Am I missing something? He? She? It? Are they now interchangeable?

On Wed, 11 Mar 2020 at 16:15, Tim Gruene > wrote:


Dear Gerard,

you are wrong. 'he'  in this context has as much information as
'someone' and
'person'. It does not refer to the sex of the person spoken about.

Best regards,
Tim

On Wednesday, March 11, 2020 4:44:47 PM CET Gerard DVD Kleywegt wrote:
 > >>>       Sorry to have taken this matter up in such a visible
manner: I
 > >>>       noticed
 > >>>
 > >>> this very wrong formula in someone's paper, and that person
then told me
 > >>> where he had found it. Having landed on that page, I didn't
know where
 > >>> to go
 > For the students:
 >
 > "someone" = systematic absence of information = 0 bits
 > "person" = systematic absence of information = 0 bits
 > "he" = 1 bit of information!
 >
 > --The other Gerard (1 bit of information!)
 >
 > **
 >                             Gerard J. Kleywegt
 >
 > 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.
 > **
 >     Little known gastromathematical curiosity: let "z" be the
 >     radius and "a" the thickness of a pizza. Then the volume
 >              of that pizza is equal to pi*z*z*a !
 > **
 >
 >

 >
 > To unsubscribe from the CCP4BB list, click the following link:
 > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

-- 
--

Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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--
Rasmus H. Fogh   Tel.: +44 (0)1223 353033
Global Phasing Ltd., Fax.: +44 (0)1223 366889
Sheraton House,
Castle Park,
Cambridge CB3 0AX
United Kingdom



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Re: [ccp4bb] [g...@globalphasing.com: [ccp4bb] An error in the IUCr Online Dictionary of Crystallography] (fwd)

2020-03-11 Thread Eleanor Dodson 
Am I missing something? He? She? It? Are they now interchangeable?

On Wed, 11 Mar 2020 at 16:15, Tim Gruene  wrote:

> Dear Gerard,
>
> you are wrong. 'he'  in this context has as much information as 'someone'
> and
> 'person'. It does not refer to the sex of the person spoken about.
>
> Best regards,
> Tim
>
> On Wednesday, March 11, 2020 4:44:47 PM CET Gerard DVD Kleywegt wrote:
> > >>>   Sorry to have taken this matter up in such a visible manner: I
> > >>>   noticed
> > >>>
> > >>> this very wrong formula in someone's paper, and that person then
> told me
> > >>> where he had found it. Having landed on that page, I didn't know
> where
> > >>> to go
> > For the students:
> >
> > "someone" = systematic absence of information = 0 bits
> > "person" = systematic absence of information = 0 bits
> > "he" = 1 bit of information!
> >
> > --The other Gerard (1 bit of information!)
> >
> > **
> > Gerard J. Kleywegt
> >
> >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.
> > **
> > Little known gastromathematical curiosity: let "z" be the
> > radius and "a" the thickness of a pizza. Then the volume
> >  of that pizza is equal to pi*z*z*a !
> > **
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>
> --
> --
> Tim Gruene
> Head of the Centre for X-ray Structure Analysis
> Faculty of Chemistry
> University of Vienna
>
> Phone: +43-1-4277-70202
>
> GPG Key ID = A46BEE1A
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>



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Re: [ccp4bb] [g...@globalphasing.com: [ccp4bb] An error in the IUCr Online Dictionary of Crystallography] (fwd)

2020-03-11 Thread Tim Gruene 
Dear Gerard,

you are wrong. 'he'  in this context has as much information as 'someone' and 
'person'. It does not refer to the sex of the person spoken about. 

Best regards,
Tim

On Wednesday, March 11, 2020 4:44:47 PM CET Gerard DVD Kleywegt wrote:
> >>>   Sorry to have taken this matter up in such a visible manner: I
> >>>   noticed
> >>> 
> >>> this very wrong formula in someone's paper, and that person then told me
> >>> where he had found it. Having landed on that page, I didn't know where
> >>> to go
> For the students:
> 
> "someone" = systematic absence of information = 0 bits
> "person" = systematic absence of information = 0 bits
> "he" = 1 bit of information!
> 
> --The other Gerard (1 bit of information!)
> 
> **
> Gerard J. Kleywegt
> 
>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.
> **
> Little known gastromathematical curiosity: let "z" be the
> radius and "a" the thickness of a pizza. Then the volume
>  of that pizza is equal to pi*z*z*a !
> **
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

-- 
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1


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Re: [ccp4bb] [g...@globalphasing.com: [ccp4bb] An error in the IUCr Online Dictionary of Crystallography] (fwd)

2020-03-11 Thread Gerard DVD Kleywegt 

  Sorry to have taken this matter up in such a visible manner: I noticed
this very wrong formula in someone's paper, and that person then told me
where he had found it. Having landed on that page, I didn't know where to go


For the students:

"someone" = systematic absence of information = 0 bits
"person" = systematic absence of information = 0 bits
"he" = 1 bit of information!

--The other Gerard (1 bit of information!)

**
   Gerard J. Kleywegt

  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.
**
   Little known gastromathematical curiosity: let "z" be the
   radius and "a" the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**



To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] [g...@globalphasing.com: [ccp4bb] An error in the IUCr Online Dictionary of Crystallography] (fwd)

2020-03-10 Thread Gerard Bricogne 
Dear Brian,

 Thank you for your reply. I think I could have provided you with the
correct formula myself ;-) but it is indeed correct now. In any case, the
verbal description I gave in my message specified it already.

 The definition in the mmCIF dictionary does look like the source of
that aberrant formula. Is it actually used somewhere as defined? That would
be scary.

 In any case, the one formula in the paper by Jones et al. cited in the
mmCIF description is a real-space R-factor, not a real-space correlation
coefficient. Some sort of monstrous recombination seems to have taken place
between the formula for an R-factor and that for a correlation coefficient,
giving rise to the eye-popping formula I spotted.

 I hope you won't mind if I post this reply to the CCP4BB again, just
for its general entertainment value. It isn't every day that one comes
across this type of typesetting hybridisation :-))) .


 With best wishes,

  Gerard.

--
On Tue, Mar 10, 2020 at 05:39:54PM +, Brian McMahon wrote:
> Dear Gerard
> 
> I've made an amendment following a version of the equation sent
> separately by Randy Read. Please review and let me know if that is
> satisfactory.
> 
> This error seems to have arisen from a transcription of a definition in the
> mmCIF/PDBx dictionary 
> (http://mmcif.pdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_struct_mon_prot.RSCC_all.html)
> which will also need updating. I'll follow that up.
> 
> Thanks for bringing this to our attention.
> 
> Best wishes
> Brian
> 
> 
> On 10/03/2020 17:11, Gerard Bricogne wrote:
> > Dear Brian,
> > 
> >   Sorry to have taken this matter up in such a visible manner: I noticed
> > this very wrong formula in someone's paper, and that person then told me
> > where he had found it. Having landed on that page, I didn't know where to go
> > next. I can't create an account because I do not have an entry in the World
> > Directory of Crystallographers.
> > 
> >   What is the best way of getting this formula corrected?
> > 
> > 
> >   With best wishes,
> > 
> >Gerard.
> > 
> > - Forwarded message from Gerard Bricogne  -
> > 
> > Date: Tue, 10 Mar 2020 14:15:33 +
> > From: Gerard Bricogne 
> > Subject: [ccp4bb] An error in the IUCr Online Dictionary of Crystallography
> > To: CCP4BB@JISCMAIL.AC.UK
> > 
> > Dear all,
> > 
> >   While we are all discussing how to "push the frontiers" of our field,
> > there seem to be some dark and dusty corners in the documentation of some
> > basic notions. For instance the formula for the real-space correlation
> > coefficient given at
> > 
> >   https://dictionary.iucr.org/Real-space_correlation_coefficient
> > 
> > is completely garbled. The absolute value signs in the denominator are
> > superfluous, although harmless since we are dealing with real numbers, but
> > the numerator is wrong in two respects:
> > 
> >   1. there should not be absolute values around the deviations from the
> >  mean of the two types of densities;
> > 
> >   2. the expression should be a single summation of products of those 
> > two
> >  types of deviation, not a product of single sums!
> > 
> > Does anyone know how to get this corrected?
> > 
> > 
> >   With best wishes,
> > 
> >Gerard.
> > 
> > 
> > 
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
> > 
> > - End forwarded message -
> > 



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