Re: [ccp4bb] very informative - Trends in Data Fabrication

[Anastassis Perrakis]

>> I still believe Prof. Dr. Hofkristallrat außer Dienst, is written as 
>> Bernhard - unless you are referring to some other guy with a >> french name 
>> Bernard. And the book indeed is a bible of xtallography.
>>Jürgen

ausser Dienst ... now I get it ... my German is a lot worse than just spelling 
names wrong ;-)
(and sorry for the 'ss' - no clue where Escet is in my keyboard)

and indeed the book is great - maybe get the publication year and count PDB 
structures before and after it ... We are in year 3 Anno Rupp ... (and no 
worries Bernhard about the errata ... the Bible likely contains many more ... 
each chapter is contradicting every other ... at least you are consistent!)

Best -

A.

[ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]

[Paul Emsley]

The PDBe page for 3k78 says:

"The experimental data has been deposited"

the data cif file says:

"data is under question"

Grump.

Is it to late to refer to data as if there were more than one of them?

Anyway, the data mtz file is here if you want to refine with it:

http://lmb.bioch.ox.ac.uk/emsley/data/r3k78sf.mtz

Paul.

Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]

[Gerard Bricogne]

Dear Paul,

 May I join the mostly silent chorus of Greek/Latin-aware grumps who
wince when seeing "data" treated as singular when it is plural. Related
instances are

 * a phenomenon (singular) vs. several phenomena (plural),
 
 * a criterion (singular) vs. several criteria (plural)
 
and many more.

 And then there is the infamous mix-up between "principal" (adjective)
and "principle" (noun, as in Principle of Least Action, or Peter's
Principle) giving rise to the favourite hero, the "Principle Investigator".

 This phenomena is now so widespread that perhaps compliance with
ancient Greek or Latin morphology is no longer a relevant criteria ;-) . 


 With best wishes,
 
  Gerard.

--
On Sun, Apr 01, 2012 at 01:05:10PM +0100, Paul Emsley wrote:
> The PDBe page for 3k78 says:
>
> "The experimental data has been deposited"
>
> the data cif file says:
>
> "data is under question"
>
> Grump.
>
> Is it to late to refer to data as if there were more than one of them?
>
> Anyway, the data mtz file is here if you want to refine with it:
>
> http://lmb.bioch.ox.ac.uk/emsley/data/r3k78sf.mtz
>
> Paul.

-- 

 ===
 * *
 * 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] very informative - Trends in Data Fabrication

[Robbie Joosten]

Dear CCP4BBers,

The PDB_REDO entry Bernhard referred to in his interesting and very thorough
article was automatically deleted because the original PDB entry was
obsoleted. Since access to the 'experimental' data of any study is
important, we have made a compressed copy of the PDB_REDO entry available at
http://www.cmbi.ru.nl/pdb_redo/others/3k78.tar.bz2 
Our apologies to those who have looked for this entry in vain.

Best wishes,
Robbie Joosten (on behalf of the PDB_REDO team)

Biochemistry
Netherlands Cancer Institute

P.S. The whole fraud thing seems to have interfered with the annual April
fools' post on CCP4BB. Let's hope this will not happen again. 





> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Michel Fodje
> Sent: Saturday, March 31, 2012 21:55
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication
> 
> Very interesting
> 
> "Response to Detection and analysis of unusual features in the structural
> model and structure-factor data of a birch pollen allergen"
> doi:10.1107/S1744309112008433
> 
> a quote from the response:
> 
> "Author Schwarzenbacher admits to the allegations of data fabrication and
> deeply apologizes to the co-authors and the scientific community for all
the
> problems this has caused
> 
> .
> 
> Note added in proof: subsequent to the acceptance of this article for
> publication, author Schwarzenbacher withdrew his admission of the
> allegations.
> "
> 
> 
> 
> 
> 
> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Bernhard Rupp (Hofkristallrat a.D.) [hofkristall...@gmail.com]
> Sent: Saturday, March 31, 2012 12:42 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication
> 
> This is an unresolved problem, and no real satisfactory solution exists,
> because the underlying reasons for zero occupancy can be different.
> For people who understand this and look at electron density, it is not a
> problem. For users who rely on some graphics program displaying only atom
> coordinates, it can be. The same holds for manipulation of B-factors,
‘trading’
> high B-factors against reduced occupancy, and other (almost always purely
> cosmetic but still confusing or inconsistent) practices.
> 
> Best, BR
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Nian Huang
> Sent: Saturday, March 31, 2012 11:29 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication
> 
> I don't model zero occupancy in my model. But can't the refinement
> programs just treat those atoms with zero occupancy as missing atoms?
> 
> Nian Huang
> On Sat, Mar 31, 2012 at 10:26 AM, Bosch, Juergen
> mailto:jubo...@jhsph.edu>> wrote:
> really fascinating, bringing back the discussion for a repository for your
> collected frames.
> 
> Jürgen
> 
> 
> Acta Cryst. (2012). F68, 366-376
> doi:10.1107/S1744309112008421 21>
> 
> Detection and analysis of unusual features in the structural model and
> structure-factor data of a birch pollen allergen B.
> Rupp bin/citedin?search_on=name&author_name=Rupp,%20B.>
> 
> Abstract: Physically improbable features in the model of the birch pollen
> structure Bet v 1d (PDB entry 3k78 bin/opdbshort?3k78>) are faithfully reproduced in electron density
> generated with the deposited structure factors, but these structure
factors
> themselves exhibit properties that are characteristic of data calculated
from a
> simple model and are inconsistent with the data and error model obtained
> through experimental measurements. The refinement of the
> 3k78model against these
> structure factors leads to an isomorphous structure different from the
> deposited model with an implausibly small R value (0.019). The abnormal
> refinement is compared with normal refinement of an isomorphous variant
> structure of Bet v 1l (PDB entry 1fm4 bin/opdbshort?1fm4>). A variety of analytical tools, including the
application
> of Diederichs plots, R plots and bulk-solvent analysis are discussed as
> promising aids in validation. The examination of the Bet v 1d structure
also
> cautions against the practice of indicating poorly defined protein chain
> residues through zero occupancies. The recommendation to preserve
> diffraction images is amplified.
> ..
> Jürgen Bosch
> Johns Hopkins University
> Bloomberg School of Public Health
> Department of Biochemistry & Molecular Biology Johns Hopkins Malaria
> Research Institute
> 615 North Wolfe Street, W8708
> Baltimore, MD 21205
> Office: +1-410-614-4742
> Lab:  +1-410-614-4894
> Fax:  +1-410-955-2926
> http://web.mac.com/bosch_lab/

Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]

[George T. DeTitta]

Perhaps the world could use a few more principle investigators?

A Buffalo view
Sent via BlackBerry by AT&T

-Original Message-
From: Gerard Bricogne 
Sender: CCP4 bulletin board 
Date: Sun, 1 Apr 2012 15:18:15 
To: 
Reply-To: Gerard Bricogne 
Subject: Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - 
Trends in Data Fabrication]

Dear Paul,

 May I join the mostly silent chorus of Greek/Latin-aware grumps who
wince when seeing "data" treated as singular when it is plural. Related
instances are

 * a phenomenon (singular) vs. several phenomena (plural),

 * a criterion (singular) vs. several criteria (plural)

and many more.

 And then there is the infamous mix-up between "principal" (adjective)
and "principle" (noun, as in Principle of Least Action, or Peter's
Principle) giving rise to the favourite hero, the "Principle Investigator".

 This phenomena is now so widespread that perhaps compliance with
ancient Greek or Latin morphology is no longer a relevant criteria ;-) .


 With best wishes,

  Gerard.

--
On Sun, Apr 01, 2012 at 01:05:10PM +0100, Paul Emsley wrote:
> The PDBe page for 3k78 says:
>
> "The experimental data has been deposited"
>
> the data cif file says:
>
> "data is under question"
>
> Grump.
>
> Is it to late to refer to data as if there were more than one of them?
>
> Anyway, the data mtz file is here if you want to refine with it:
>
> http://lmb.bioch.ox.ac.uk/emsley/data/r3k78sf.mtz
>
> Paul.

--

 ===
 * *
 * 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] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]

[Adrian Goldman]

You can find all the principle investigators you want collecting datums ;) at 
the ESRF,  as that is how the French spell it on the application form for beam 
time!  (Unless it has _finally_ been corrected: haven't checked since I 
submitted my last BAG application in April.)

Adrian


On 1 Apr 2012, at 17:52, George T. DeTitta wrote:

> Perhaps the world could use a few more principle investigators?
> 
> A Buffalo view
> Sent via BlackBerry by AT&T
> 
> -Original Message-
> From: Gerard Bricogne 
> Sender: CCP4 bulletin board 
> Date: Sun, 1 Apr 2012 15:18:15 
> To: 
> Reply-To: Gerard Bricogne 
> Subject: Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative 
> - Trends in Data Fabrication]
> 
> Dear Paul,
> 
> May I join the mostly silent chorus of Greek/Latin-aware grumps who
> wince when seeing "data" treated as singular when it is plural. Related
> instances are
> 
> * a phenomenon (singular) vs. several phenomena (plural),
> 
>* a criterion (singular) vs. several criteria (plural)
> 
> and many more.
> 
> And then there is the infamous mix-up between "principal" (adjective)
> and "principle" (noun, as in Principle of Least Action, or Peter's
> Principle) giving rise to the favourite hero, the "Principle Investigator".
> 
> This phenomena is now so widespread that perhaps compliance with
> ancient Greek or Latin morphology is no longer a relevant criteria ;-) .
> 
> 
> With best wishes,
> 
>  Gerard.
> 
> --
> On Sun, Apr 01, 2012 at 01:05:10PM +0100, Paul Emsley wrote:
>> The PDBe page for 3k78 says:
>> 
>> "The experimental data has been deposited"
>> 
>> the data cif file says:
>> 
>> "data is under question"
>> 
>> Grump.
>> 
>> Is it to late to refer to data as if there were more than one of them?
>> 
>> Anyway, the data mtz file is here if you want to refine with it:
>> 
>> http://lmb.bioch.ox.ac.uk/emsley/data/r3k78sf.mtz
>> 
>> Paul.
> 
> --
> 
> ===
> * *
> * 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] very informative - Trends in Data Fabrication

[Paul Emsley]

On 31/03/12 23:08, Kevin Jin wrote:



I really wish PDB could have some people to review those important 
structures, like paper reviewer.




So do the wwPDB, I would imagine.

But they can't just magic funding and positions into existence...

If the coordinate is downloaded for modeling and docking, people may 
not check the density and model by themself. However this is not the 
worst case, since the original data was fabricated.



1. All of data was correct and real,



Hmmm...

 It will be very difficult for people to check the density and 
coordinated if he/she is not a well-trained crystallographer.


I hope and believe that this is not the case.  Even basically-trained 
crystallographers should be able to calculate and interpret difference 
maps of the kind described by Bernhard.  And with the EDS and PDB_REDO 
server, one does not even need to know how to make generate a difference 
map...


Paul.

Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]

[Patrick Loll]

Hear, hear! I'm glad to know I'm not the last grump left standing. When I raise 
this point every year, my students regard me with bemused stares, as though 
they've just seen a coelacanth swim past their window...


On 1 Apr 2012, at 10:18 AM, Gerard Bricogne wrote:

> Dear Paul,
> 
> May I join the mostly silent chorus of Greek/Latin-aware grumps who
> wince when seeing "data" treated as singular when it is plural. Related
> instances are
> 
> * a phenomenon (singular) vs. several phenomena (plural),
>
>* a criterion (singular) vs. several criteria (plural)
>
> and many more.
> 
> And then there is the infamous mix-up between "principal" (adjective)
> and "principle" (noun, as in Principle of Least Action, or Peter's
> Principle) giving rise to the favourite hero, the "Principle Investigator".
> 
> This phenomena is now so widespread that perhaps compliance with
> ancient Greek or Latin morphology is no longer a relevant criteria ;-) . 
> 
> 
> With best wishes,
> 
>  Gerard.
> 
> --
> On Sun, Apr 01, 2012 at 01:05:10PM +0100, Paul Emsley wrote:
>> The PDBe page for 3k78 says:
>> 
>> "The experimental data has been deposited"
>> 
>> the data cif file says:
>> 
>> "data is under question"
>> 
>> Grump.
>> 
>> Is it to late to refer to data as if there were more than one of them?
>> 
>> Anyway, the data mtz file is here if you want to refine with it:
>> 
>> http://lmb.bioch.ox.ac.uk/emsley/data/r3k78sf.mtz
>> 
>> Paul.
> 
> -- 
> 
> ===
> * *
> * 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] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]

[VAN RAAIJ , MARK JOHAN]

another singular/plural grump:
Recently we can read: "phage are".
Phage is singular, the plural is phages (and this does not have that  
much to do with latin or greek).

more reading:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3109450/

Quoting Paul Emsley:


The PDBe page for 3k78 says:

"The experimental data has been deposited"

the data cif file says:

"data is under question"

Grump.

Is it to late to refer to data as if there were more than one of them?

Anyway, the data mtz file is here if you want to refine with it:

http://lmb.bioch.ox.ac.uk/emsley/data/r3k78sf.mtz

Paul.





Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoléculas
Centro Nacional de Biotecnología - CSIC
c/Darwin 3, Campus Cantoblanco
28049 Madrid
tel. 91 585 4616
email: mjvanra...@cnb.csic.es

Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]

[Antony Oliver]

Think the jury might be out on this one... A quick snip from WikiDictionary...

"The plural word phages refers to different types of phage, whereas in common 
usage the word phage can be both singular and plural, referring in the plural 
sense to particles of the same type of phage." Maloy et al: Microbial Genetics, 
2nd ed., 1984

Tony.

---
Mobile Account
---

On 1 Apr 2012, at 16:29, "VAN RAAIJ , MARK JOHAN" 
mailto:mjvanra...@cnb.csic.es>> wrote:

another singular/plural grump:
Recently we can read: "phage are".
Phage is singular, the plural is phages (and this does not have that much to do 
with latin or greek).
more reading:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3109450/

Quoting Paul Emsley:

The PDBe page for 3k78 says:

"The experimental data has been deposited"

the data cif file says:

"data is under question"

Grump.

Is it to late to refer to data as if there were more than one of them?

Anyway, the data mtz file is here if you want to refine with it:

http://lmb.bioch.ox.ac.uk/emsley/data/r3k78sf.mtz

Paul.




Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoléculas
Centro Nacional de Biotecnología - CSIC
c/Darwin 3, Campus Cantoblanco
28049 Madrid
tel. 91 585 4616
email: mjvanra...@cnb.csic.es

Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]

[Gerard DVD Kleywegt]

Is it to late to refer to data as if there were more than one of them?


Is it too late to explain the difference between "to" and "too"?

--A much mellowed CD

Re: [ccp4bb] one datum many data?

[Robert Blessing]

How can "spectrum" and "spectra" have been overlooked in this thread?

Síocháin!  Sláinte!
  In Irish:  Peace!  Health!
  Pronounced roughly "Shee'-kahn", "Slawn'-tche".

Bob

Robert H. Blessing, Ph.D.
Senior Research Scientist
  Hauptman-Woodward Medical Research Institute, Inc.
Professor of Structural Biology and Research Professor of Chemistry
Director of Graduate Studies in Structural Biology
Interim Chairman of the Department of Structural Biology
  State University of New York at Buffalo

Hauptman-Woodward Institute
700 Ellicott Street
Buffalo, New York 14203, USA
  Phone  716-898-8613
  Fax716-898-8660
  eMail  bless...@hwi.buffalo.edu
  Internet   http://www.hwi.buffalo.edu

Re: [ccp4bb] one datum many data?

[VAN RAAIJ , MARK JOHAN]

and using "dice" for the singular "die"

Quoting Robert Blessing:


How can "spectrum" and "spectra" have been overlooked in this thread?

Síocháin!  Sláinte!
  In Irish:  Peace!  Health!
  Pronounced roughly "Shee'-kahn", "Slawn'-tche".

Bob

Robert H. Blessing, Ph.D.
Senior Research Scientist
  Hauptman-Woodward Medical Research Institute, Inc.
Professor of Structural Biology and Research Professor of Chemistry
Director of Graduate Studies in Structural Biology
Interim Chairman of the Department of Structural Biology
  State University of New York at Buffalo

Hauptman-Woodward Institute
700 Ellicott Street
Buffalo, New York 14203, USA
  Phone  716-898-8613
  Fax716-898-8660
  eMail  bless...@hwi.buffalo.edu
  Internet   http://www.hwi.buffalo.edu





Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoléculas
Centro Nacional de Biotecnología - CSIC
c/Darwin 3, Campus Cantoblanco
28049 Madrid
tel. 91 585 4616
email: mjvanra...@cnb.csic.es

Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]

[David Schuller]

On 04/01/12 10:18, Gerard Bricogne wrote:

Dear Paul,

  May I join the mostly silent chorus of Greek/Latin-aware grumps who
wince when seeing "data" treated as singular when it is plural.

When it are plural?
At any rate, I heard a Nobel laureate use it incorrectly just two days ago.

--
===
All Things Serve the Beam
===
   David J. Schuller
   modern man in a post-modern world
   MacCHESS, Cornell University
   schul...@cornell.edu

Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]

[Gerard Bricogne]

On Sun, Apr 01, 2012 at 01:18:15PM -0400, David Schuller wrote:
> On 04/01/12 10:18, Gerard Bricogne wrote:
>> Dear Paul,
>>
>>   May I join the mostly silent chorus of Greek/Latin-aware grumps who
>> wince when seeing "data" treated as singular when it is plural.
> When it are plural?

 Good nit-picking :-) . In my mind the quotes around "data" would have
had the same effect as writing 'the word "data"', and referring to that word
by the 'it'. So there is only one word, while its grammatical number is
plural. 


> At any rate, I heard a Nobel laureate use it incorrectly just two days ago.

 We shouldn't learn to write by imitating Nobel laureates, then.


 With best wishes,
 
  Gerard.

> -- 
> ===
> All Things Serve the Beam
> ===
>David J. Schuller
>modern man in a post-modern world
>MacCHESS, Cornell University
>schul...@cornell.edu

[ccp4bb]

[protein chemistry]

Dear All,

I have one query regarding the atom number in the coordinates. Before i
began with my coordinate submission i need to put TER cap at the end of
chains/polymers, but that may lead to change in atom number for the
subsequent residues/molecules. i need to know is there any way to do this
or i shall leave it and submit the coordinates directly.

Thanks in advance

Abraham

Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]

[Phoebe Rice]

Ah, an old pet peeve resurfaces!

English is complicated and "data" is by now an English word.

To use a somewhat strained analogy, at the quantum level, the word has a 
singular and a plural form, and at the classical-mechanics level, the word is a 
mass noun.  

Most crystallographers use the word "data" as a mass noun - that is, the syntax 
of "data" follows that of "gravel" or "mud", not that of "pebble/pebbles".  
People 
who pounce on the phrase "data is" routinely say "data collection" and "data 
processing".  But note that the proper way to construct compound nouns such as 
those is to use the singular form - one would never say "rocks collection" or 
"apples picking".  So if we have to say "data are" then we should be discussing 
how (not) to fabricate a "datum set".  Also note that when people come back 
from the synchrotron, we ask "how much data did you collect" not "how many".  
"Much" is generally used with mass nouns.

That doesn't mean we can't ALSO use the word as one with discrete singular and 
plural forms, especially when we have a few, individual observations rather 
than 
a huge pile that blurs into an aggregate.  In that case, I see nothing 
incorrect 
about discussing an individual datum and using "data" as the plural form. 

Sometimes it is the artificial, over-simplified rule that is stupid, not the 
native 
speakers of a language.

=
Phoebe A. Rice
Dept. of Biochemistry & Molecular Biology
The University of Chicago
phone 773 834 1723
http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alp
habetically.php?faculty_id=123
http://www.rsc.org/shop/books/2008/9780854042722.asp


 Original message 
>Date: Sun, 1 Apr 2012 13:05:10 +0100
>From: CCP4 bulletin board  (on behalf of Paul 
Emsley )
>Subject: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - 
Trends in Data Fabrication]  
>To: CCP4BB@JISCMAIL.AC.UK
>
>The PDBe page for 3k78 says:
>
>"The experimental data has been deposited"
>
>the data cif file says:
>
>"data is under question"
>
>Grump.
>
>Is it to late to refer to data as if there were more than one of them?
>
>Anyway, the data mtz file is here if you want to refine with it:
>
>http://lmb.bioch.ox.ac.uk/emsley/data/r3k78sf.mtz
>
>Paul.

Re: [ccp4bb] very informative - Trends in Data Fabrication

[Bryan Lepore]

On Sat, Mar 31, 2012 at 6:08 PM, Kevin Jin  wrote:

> I have seen several stories like this. Here is an open letter to Nature.
>
> http://www.jinkai.org/AAD/AAD_letter_2_nature.html
>

I'd like to understand this better : please explain precisely, on this
forum, the connection being made between the following two subjects :

[A]  "Detection and analysis of unusual features in the structural model
and structure-factor data of a birch pollen allergen", Acta F 68, 366, 2012

[B] Acetoacetate Decarboxylase (AAD).

-Bryan

Re: [ccp4bb] very informative - Trends in Data Fabrication

[Kevin Jin]

“I hope and believe that this is not the case.  Even basically-trained
crystallographers should be able to calculate andinterpret difference
maps of the kind described by Bernhard.  And with the EDS and PDB_REDO
server, one does not even need to know how to make generate a difference map
...”

*You are right*!

Actually, I am not an experienced protein crystallographer. I have learnt a
lot from CCP4BB. I may have paid too much attention to bonding angle and
bond length, like in small molecule. This may be an example to share with
you.

When I worked on those nitroreductase complexed with FMN in 2009 (?), I
always observed that the flavin ring presented a strange geometry after
refinement. Indeed, I had used the definition of FMN from CCP4 library all
the time.

In some cases, the methyl group at position of either 7a or 8a was bent off
the aromatic ring, if the whole the rest of flavin was restrained in a flat
plane.  According to my limited knowledge from organic chemistry, carbon of
7 and 8 on the flavin ring is sp2 hybridized in a coplanar manner. How
could those methyl groups be bent as sp3 hybridization? Any chemistry
behind?

With increased resolution (1.6 ~ 1.8 Ang), I observed that the electron
density map was a bent along the N5-N10 axis. The bend angle was around ~16
degree.   Again, I questioned myself why it was bent? Should this be
correct?

According to my limited knowledge in chemistry, N10 should be sp3
configuration even if FMN is in its oxidization form, in which the flavin
ring should be bent. A quick “google” immediately gave me a link to a very
nice paper published by David W. Rodgers in 2002.

http://www.jbc.org/content/277/13/11513.full.pdf+html

According to this paper, Yes!  “*In the oxidized enzyme, the flavin ring
system adopts a strongly bent (16°) conformation, and the bend increases
(25°) in the reduced form of the enzyme*,…”

When I reported this in the group meeting, I was laughed and told that this
is just a model bias. It was over interpreted.  Nobody has such sharp
vision on electron density map.  If this was correct, why nobody could find
this and report to CCP4 within last 7 years?

Eventually, a senior team member emailed to CCP4 about this issue. Since
then, the definition of FMN was updated, according to my suggestion.

I was asked “how did you find it?”……. “why you believed you are so right?”
 I really don’t how to answer.

*Je pense donc je suis*

Kevin


On Sun, Apr 1, 2012 at 8:09 AM, Paul Emsley 
wrote:
> On 31/03/12 23:08, Kevin Jin wrote:
>
>
> I really wish PDB could have some people to review those important
> structures, like paper reviewer.
>
>
> So do the wwPDB, I would imagine.
>
> But they can't just magic funding and positions into existence...
>
> If the coordinate is downloaded for modeling and docking, people may not
> check the density and model by themself. However this is not the worst
case,
> since the original data was fabricated.
>
>
> 1. All of data was correct and real,
>
>
> Hmmm...
>
>  It will be very difficult for people to check the density and coordinated
> if he/she is not a well-trained crystallographer.
>
>
> I hope and believe that this is not the case.  Even basically-trained
> crystallographers should be able to calculate and interpret difference
maps
> of the kind described by Bernhard.  And with the EDS and PDB_REDO server,
> one does not even need to know how to make generate a difference map...
>
> Paul.
>
>



-- 
Kevin Jin

Sharing knowledge each other is always very joyful..

Website: http://www.jinkai.org/

Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]

[Bosch, Juergen]

Grumpy old men :-)

I feel hijacked or is hijacketed ?
Don't we all speak and write perfect BE (not as in British English, but more 
like Bad English) ?

May the impact factor for TiDF continue to be very low.

Jürgen

..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-2926
http://web.mac.com/bosch_lab/

Re: [ccp4bb] very informative - Trends in Data Fabrication

[Bernhard Rupp (Hofkristallrat a.D.)]

 

Je pense donc je suis

 

Kevin

 

Cogito ergo erro.

 

BR

Re: [ccp4bb] very informative - Trends in Data Fabrication

[Kendall Nettles]

What is the single Latin word for troll?

Kendall

On Apr 1, 2012, at 3:06 PM, "Kevin Jin" 
mailto:kevin...@gmail.com>> wrote:

“I hope and believe that this is not the case.  Even basically-trained 
crystallographers should be able to calculate andinterpret difference maps 
of the kind described by Bernhard.  And with the EDS and PDB_REDO server, one 
does not even need to know how to make generate a difference map...”

You are right!

Actually, I am not an experienced protein crystallographer. I have learnt a lot 
from CCP4BB. I may have paid too much attention to bonding angle and bond 
length, like in small molecule. This may be an example to share with you.

When I worked on those nitroreductase complexed with FMN in 2009 (?), I always 
observed that the flavin ring presented a strange geometry after refinement. 
Indeed, I had used the definition of FMN from CCP4 library all the time.

In some cases, the methyl group at position of either 7a or 8a was bent off the 
aromatic ring, if the whole the rest of flavin was restrained in a flat plane.  
According to my limited knowledge from organic chemistry, carbon of 7 and 8 on 
the flavin ring is sp2 hybridized in a coplanar manner. How could those methyl 
groups be bent as sp3 hybridization? Any chemistry behind?

With increased resolution (1.6 ~ 1.8 Ang), I observed that the electron density 
map was a bent along the N5-N10 axis. The bend angle was around ~16 degree.   
Again, I questioned myself why it was bent? Should this be correct?

According to my limited knowledge in chemistry, N10 should be sp3 configuration 
even if FMN is in its oxidization form, in which the flavin ring should be 
bent. A quick “google” immediately gave me a link to a very nice paper 
published by David W. Rodgers in 2002.

http://www.jbc.org/content/277/13/11513.full.pdf+html

According to this paper, Yes!  “In the oxidized enzyme, the flavin ring system 
adopts a strongly bent (16°) conformation, and the bend increases (25°) in the 
reduced form of the enzyme,…”

When I reported this in the group meeting, I was laughed and told that this is 
just a model bias. It was over interpreted.  Nobody has such sharp vision on 
electron density map.  If this was correct, why nobody could find this and 
report to CCP4 within last 7 years?

Eventually, a senior team member emailed to CCP4 about this issue. Since then, 
the definition of FMN was updated, according to my suggestion.

I was asked “how did you find it?”……. “why you believed you are so right?”  I 
really don’t how to answer.

Je pense donc je suis

Kevin


On Sun, Apr 1, 2012 at 8:09 AM, Paul Emsley 
mailto:paul.ems...@bioch.ox.ac.uk>> wrote:
> On 31/03/12 23:08, Kevin Jin wrote:
>
>
> I really wish PDB could have some people to review those important
> structures, like paper reviewer.
>
>
> So do the wwPDB, I would imagine.
>
> But they can't just magic funding and positions into existence...
>
> If the coordinate is downloaded for modeling and docking, people may not
> check the density and model by themself. However this is not the worst case,
> since the original data was fabricated.
>
>
> 1. All of data was correct and real,
>
>
> Hmmm...
>
>  It will be very difficult for people to check the density and coordinated
> if he/she is not a well-trained crystallographer.
>
>
> I hope and believe that this is not the case.  Even basically-trained
> crystallographers should be able to calculate and interpret difference maps
> of the kind described by Bernhard.  And with the EDS and PDB_REDO server,
> one does not even need to know how to make generate a difference map...
>
> Paul.
>
>



--
Kevin Jin

Sharing knowledge each other is always very joyful..

Website: http://www.jinkai.org/

Re: [ccp4bb] very informative - Trends in Data Fabrication

[David Briggs]

Trollus, Trollum, Trolli, Trollo, Trolli, Trollos, Trollorum, Trollis.



David C. Briggs PhD
Father, Structural Biologist and Sceptic

University of Manchester E-mail:
david.c.bri...@manchester.ac.uk

Webs : http://flavors.me/xtaldave
Twitter: @xtaldave
Skype: DocDCB




On 1 April 2012 21:27, Kendall Nettles  wrote:
> What is the single Latin word for troll?
>
> Kendall
>
> On Apr 1, 2012, at 3:06 PM, "Kevin Jin"  wrote:
>
> “I hope and believe that this is not the case.  Even basically-trained
> crystallographers should be able to calculate and    interpret difference
> maps of the kind described by Bernhard.  And with the EDS and PDB_REDO
> server, one does not even need to know how to make generate a difference
> map...”
>
> You are right!
>
> Actually, I am not an experienced protein crystallographer. I have learnt a
> lot from CCP4BB. I may have paid too much attention to bonding angle and
> bond length, like in small molecule. This may be an example to share with
> you.
>
> When I worked on those nitroreductase complexed with FMN in 2009 (?), I
> always observed that the flavin ring presented a strange geometry after
> refinement. Indeed, I had used the definition of FMN from CCP4 library all
> the time.
>
> In some cases, the methyl group at position of either 7a or 8a was bent off
> the aromatic ring, if the whole the rest of flavin was restrained in a flat
> plane.  According to my limited knowledge from organic chemistry, carbon of
> 7 and 8 on the flavin ring is sp2 hybridized in a coplanar manner. How could
> those methyl groups be bent as sp3 hybridization? Any chemistry behind?
>
> With increased resolution (1.6 ~ 1.8 Ang), I observed that the electron
> density map was a bent along the N5-N10 axis. The bend angle was around ~16
> degree.   Again, I questioned myself why it was bent? Should this be
> correct?
>
> According to my limited knowledge in chemistry, N10 should be sp3
> configuration even if FMN is in its oxidization form, in which the flavin
> ring should be bent. A quick “google” immediately gave me a link to a very
> nice paper published by David W. Rodgers in 2002.
>
> http://www.jbc.org/content/277/13/11513.full.pdf+html
>
> According to this paper, Yes!  “In the oxidized enzyme, the flavin ring
> system adopts a strongly bent (16°) conformation, and the bend increases
> (25°) in the reduced form of the enzyme,…”
>
> When I reported this in the group meeting, I was laughed and told that this
> is just a model bias. It was over interpreted.  Nobody has such sharp vision
> on electron density map.  If this was correct, why nobody could find this
> and report to CCP4 within last 7 years?
>
> Eventually, a senior team member emailed to CCP4 about this issue. Since
> then, the definition of FMN was updated, according to my suggestion.
>
> I was asked “how did you find it?”……. “why you believed you are so right?”
>  I really don’t how to answer.
>
> Je pense donc je suis
>
> Kevin
>
>
> On Sun, Apr 1, 2012 at 8:09 AM, Paul Emsley 
> wrote:
>> On 31/03/12 23:08, Kevin Jin wrote:
>>
>>
>> I really wish PDB could have some people to review those important
>> structures, like paper reviewer.
>>
>>
>> So do the wwPDB, I would imagine.
>>
>> But they can't just magic funding and positions into existence...
>>
>> If the coordinate is downloaded for modeling and docking, people may not
>> check the density and model by themself. However this is not the worst
>> case,
>> since the original data was fabricated.
>>
>>
>> 1. All of data was correct and real,
>>
>>
>> Hmmm...
>>
>>  It will be very difficult for people to check the density and coordinated
>> if he/she is not a well-trained crystallographer.
>>
>>
>> I hope and believe that this is not the case.  Even basically-trained
>> crystallographers should be able to calculate and interpret difference
>> maps
>> of the kind described by Bernhard.  And with the EDS and PDB_REDO server,
>> one does not even need to know how to make generate a difference map...
>>
>> Paul.
>>
>>
>
>
>
> --
> Kevin Jin
>
> Sharing knowledge each other is always very joyful..
>
> Website: http://www.jinkai.org/
>
>
>

Re: [ccp4bb] very informative - Trends in Data Fabrication

[Bernhard Rupp (Hofkristallrat a.D.)]

orcus impudens

 

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kendall 
Nettles
Sent: Sunday, April 01, 2012 1:28 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication

 

What is the single Latin word for troll?

Kendall


On Apr 1, 2012, at 3:06 PM, "Kevin Jin"  wrote:

“I hope and believe that this is not the case.  Even basically-trained 
crystallographers should be able to calculate andinterpret difference maps 
of the kind described by Bernhard.  And with the EDS and PDB_REDO server, one 
does not even need to know how to make generate a difference map...”

 

You are right!  

 

Actually, I am not an experienced protein crystallographer. I have learnt a lot 
from CCP4BB. I may have paid too much attention to bonding angle and bond 
length, like in small molecule. This may be an example to share with you. 

 

When I worked on those nitroreductase complexed with FMN in 2009 (?), I always 
observed that the flavin ring presented a strange geometry after refinement. 
Indeed, I had used the definition of FMN from CCP4 library all the time.

 

In some cases, the methyl group at position of either 7a or 8a was bent off the 
aromatic ring, if the whole the rest of flavin was restrained in a flat plane.  
According to my limited knowledge from organic chemistry, carbon of 7 and 8 on 
the flavin ring is sp2 hybridized in a coplanar manner. How could those methyl 
groups be bent as sp3 hybridization? Any chemistry behind?

 

With increased resolution (1.6 ~ 1.8 Ang), I observed that the electron density 
map was a bent along the N5-N10 axis. The bend angle was around ~16 degree.   
Again, I questioned myself why it was bent? Should this be correct?

 

According to my limited knowledge in chemistry, N10 should be sp3 configuration 
even if FMN is in its oxidization form, in which the flavin ring should be 
bent. A quick “google” immediately gave me a link to a very nice paper 
published by David W. Rodgers in 2002.  

 

http://www.jbc.org/content/277/13/11513.full.pdf+html

 

According to this paper, Yes!  “In the oxidized enzyme, the flavin ring system 
adopts a strongly bent (16°) conformation, and the bend increases (25°) in the 
reduced form of the enzyme,…”

 

When I reported this in the group meeting, I was laughed and told that this is 
just a model bias. It was over interpreted.  Nobody has such sharp vision on 
electron density map.  If this was correct, why nobody could find this and 
report to CCP4 within last 7 years? 

 

Eventually, a senior team member emailed to CCP4 about this issue. Since then, 
the definition of FMN was updated, according to my suggestion. 

 

I was asked “how did you find it?”……. “why you believed you are so right?”  I 
really don’t how to answer. 

 

Je pense donc je suis

 

Kevin

 

 

On Sun, Apr 1, 2012 at 8:09 AM, Paul Emsley  wrote:

> On 31/03/12 23:08, Kevin Jin wrote:

> 

> 

> I really wish PDB could have some people to review those important

> structures, like paper reviewer.

> 

> 

> So do the wwPDB, I would imagine. 

> 

> But they can't just magic funding and positions into existence...

> 

> If the coordinate is downloaded for modeling and docking, people may not

> check the density and model by themself. However this is not the worst case,

> since the original data was fabricated.

> 

> 

> 1. All of data was correct and real,

> 

> 

> Hmmm...

> 

>  It will be very difficult for people to check the density and coordinated

> if he/she is not a well-trained crystallographer.

> 

> 

> I hope and believe that this is not the case.  Even basically-trained

> crystallographers should be able to calculate and interpret difference maps

> of the kind described by Bernhard.  And with the EDS and PDB_REDO server,

> one does not even need to know how to make generate a difference map...

> 

> Paul.

> 

> 

 

 

 

-- 

Kevin Jin

 

Sharing knowledge each other is always very joyful..

 

Website: http://www.jinkai.org/

 

 

 

Re: [ccp4bb] very informative - Trends in Data Fabrication

[Ethan Merritt]

On Sunday, 01 April 2012, Kendall Nettles wrote:
> 
> What is the single Latin word for troll?
> 
> Kendall
> 
According to Google Translate, it is Troglodytarum.
But I'm dubious.  
I thought trolls lived under bridges rather than in caves.
Except for the ones who inhabit the internet, of course.

Ethan

Re: [ccp4bb] very informative - Trends in Data Fabrication

[Philippe DUMAS]

David Briggs  a écrit :


Trollus, Trollum, Trolli, Trollo, Trolli, Trollos, Trollorum, Trollis.




Should we say "Alea data est" or "Alea data sunt" ?



Philippe DUMAS

Re: [ccp4bb] very informative - Trends in Data Fabrication

[Gerard DVD Kleywegt]

http://trololololololololololo.com/


Trollus, Trollum, Trolli, Trollo, Trolli, Trollos, Trollorum, Trollis.



David C. Briggs PhD
Father, Structural Biologist and Sceptic

University of Manchester E-mail:
david.c.bri...@manchester.ac.uk

Webs : http://flavors.me/xtaldave
Twitter: @xtaldave
Skype: DocDCB




On 1 April 2012 21:27, Kendall Nettles  wrote:

What is the single Latin word for troll?

Kendall

On Apr 1, 2012, at 3:06 PM, "Kevin Jin"  wrote:

?I hope and believe that this is not the case.  Even basically-trained
crystallographers should be able to calculate and    interpret difference
maps of the kind described by Bernhard.  And with the EDS and PDB_REDO
server, one does not even need to know how to make generate a difference
map...?

You are right!

Actually, I am not an experienced protein crystallographer. I have learnt a
lot from CCP4BB. I may have paid too much attention to bonding angle and
bond length, like in small molecule. This may be an example to share with
you.

When I worked on those nitroreductase complexed with FMN in 2009 (?), I
always observed that the flavin ring presented a strange geometry after
refinement. Indeed, I had used the definition of FMN from CCP4 library all
the time.

In some cases, the methyl group at position of either 7a or 8a was bent off
the aromatic ring, if the whole the rest of flavin was restrained in a flat
plane.  According to my limited knowledge from organic chemistry, carbon of
7 and 8 on the flavin ring is sp2 hybridized in a coplanar manner. How could
those methyl groups be bent as sp3 hybridization? Any chemistry behind?

With increased resolution (1.6 ~ 1.8 Ang), I observed that the electron
density map was a bent along the N5-N10 axis. The bend angle was around ~16
degree.   Again, I questioned myself why it was bent? Should this be
correct?

According to my limited knowledge in chemistry, N10 should be sp3
configuration even if FMN is in its oxidization form, in which the flavin
ring should be bent. A quick ?google? immediately gave me a link to a very
nice paper published by David W. Rodgers in 2002.

http://www.jbc.org/content/277/13/11513.full.pdf+html

According to this paper, Yes!  ?In the oxidized enzyme, the flavin ring
system adopts a strongly bent (16?) conformation, and the bend increases
(25?) in the reduced form of the enzyme,??

When I reported this in the group meeting, I was laughed and told that this
is just a model bias. It was over interpreted.  Nobody has such sharp vision
on electron density map.  If this was correct, why nobody could find this
and report to CCP4 within last 7 years?

Eventually, a senior team member emailed to CCP4 about this issue. Since
then, the definition of FMN was updated, according to my suggestion.

I was asked ?how did you find it. ?why you believed you are so right??
 I really don?t how to answer.

Je pense donc je suis

Kevin


On Sun, Apr 1, 2012 at 8:09 AM, Paul Emsley 
wrote:

On 31/03/12 23:08, Kevin Jin wrote:


I really wish PDB could have some people to review those important
structures, like paper reviewer.


So do the wwPDB, I would imagine.

But they can't just magic funding and positions into existence...

If the coordinate is downloaded for modeling and docking, people may not
check the density and model by themself. However this is not the worst
case,
since the original data was fabricated.


1. All of data was correct and real,


Hmmm...

 It will be very difficult for people to check the density and coordinated
if he/she is not a well-trained crystallographer.


I hope and believe that this is not the case.  Even basically-trained
crystallographers should be able to calculate and interpret difference
maps
of the kind described by Bernhard.  And with the EDS and PDB_REDO server,
one does not even need to know how to make generate a difference map...

Paul.






--
Kevin Jin

Sharing knowledge each other is always very joyful..

Website: http://www.jinkai.org/








Best wishes,

--Gerard

**
   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 !
**

Re: [ccp4bb] very informative - Trends in Data Fabrication

[Artem Evdokimov]

I can't resist asking: If we assume that the data fabrication
techniques and the techniques for discovery of such activities should
have the same sort of arms race as the development of viruses and
anti-malvare software (but of course on a much more modest scale since
structural biology is a relatively niche discipline) - can we then
speculate further that eventually the most sophisticated fabrication
techniques would be equivalent to de novo structure prediction :) It's
really too bad that there's no real money in this (again, relatively
speaking - not as much money as there is in software development),
because if there was then the structural biology equivalent of 'virus
hackers' would in reality approximate the same development trajectory
as the most successful (and legitimate) protein modelers. Given the
ingenuity of hackers and like-minded people in general, I sometimes
wonder if this isn't a better way to develop structure prediction
tools...

Artem

On Sun, Apr 1, 2012 at 10:09 AM, Paul Emsley  wrote:
> On 31/03/12 23:08, Kevin Jin wrote:
>
>
> I really wish PDB could have some people to review those important
> structures, like paper reviewer.
>
>
> So do the wwPDB, I would imagine.
>
> But they can't just magic funding and positions into existence...
>
> If the coordinate is downloaded for modeling and docking, people may not
> check the density and model by themself. However this is not the worst case,
> since the original data was fabricated.
>
>
> 1. All of data was correct and real,
>
>
> Hmmm...
>
>  It will be very difficult for people to check the density and coordinated
> if he/she is not a well-trained crystallographer.
>
>
> I hope and believe that this is not the case.  Even basically-trained
> crystallographers should be able to calculate and interpret difference maps
> of the kind described by Bernhard.  And with the EDS and PDB_REDO server,
> one does not even need to know how to make generate a difference map...
>
> Paul.
>
>