Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures...

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Error in CAD during ARP/wWARP run in sharp/autoSHARP - also posted in sharp discuss
From: Narayanan Ramasubbu ramasun1 {- at -} UMDNJ {- dot -} EDU
Date: 2009-12-13

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Subject: Validation and maps (was: Retraction of 12 Structures...)
From: Robbie Joosten rjoosten {- at -} CMBI {- dot -} RU {- dot -} NL
Date: 2009-12-13

Subject: Re: FW: pdb-l: Retraction of 12 Structures...
From: Nicholas M Glykos glykos {- at -} MBG {- dot -} DUTH {- dot -} GR
Date: 2009-12-13

Dear Robbie, List,

This thread is steadily diverging. Apologies for my contribution to its
diversification.

> Who knows what they did to the maps in terms of (unwarrented) density
> modefication to make them look cleaner?
>
> The advantage of the EDS is that it is impartial and
> uniform. The maps are generated in a clear and well-described way.

I agree with you that map deposition is probably a waste of resources.

I strongly disagree, though, with the existence of validation tools that
have strong views about how best I should do science. For example, your
sentence above imply that the validation tool is more fit (than myself) to
decide which maps I should be looking at. Which means that if I chose to
calculate (and view) not the simple FFT-derived map, but its maximum
entropy estimate, I am in danger of being accused that 'I did something to
the maps to make them look cleaner', where in fact, I'm just doing a
better job out of the existing data than the validation tool (which
probably generate maps in a clear, well-described and wrong way :-)

The take home message of what I'm saying is this: We should not be
deterred from practising our craft as best as we could, even if that
implies that our models contain information that a validation tool can not
reproduce. It is only fair that a well-informed and well-educated human
being can do a better job than a fixed-frozen automated procedure. Fraud
is a moral issue, and can not (and should not) be used as an excuse for
converting validation tools to the sacred holders of scientific standards.

My twocents,
Nicholas

--

Dr Nicholas M. Glykos, Department of Molecular Biology
and Genetics, Democritus University of Thrace, University Campus,
Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Error in CAD during ARP/wWARP run in sharp/autoSHARP - also posted in sharp discuss
From: Narayanan Ramasubbu ramasun1 {- at -} UMDNJ {- dot -} EDU
Date: 2009-12-13

Next message:
Subject: Validation and maps (was: Retraction of 12 Structures...)
From: Robbie Joosten rjoosten {- at -} CMBI {- dot -} RU {- dot -} NL
Date: 2009-12-13