Hi Fellows,

I was attending the inaugural meeting of the Data Deposition Working Group
in Madrid. They are aware of the various points raised, and a
document/recommendation has been prepared that I assume will be soon made
public (John?). Amount of data seems not an insurmountable technical
problem. The most important point is that the data are getting consistently
better and contain more information than we currently make use of. Just
think of diffuse solvent contributions, commensurate and incommensurate
superstructures, split reflections,  and similar stuff that presently just
gets indexed away. Better data processing software will certainly be
developed and will provide a better data model, ultimately allowing better
structure models. At the same time, almost all forgery issues disappear
automatically as an added (but imho minor) bonus.  

Cheers, BR

PS: on a cynical note, what makes one believe that data processing is
carried out at any higher level of competency than say the refinement? The
only comfort here is that when it is done immediately by the beamline
fellows, it is probably done well. In any case, maybe REPROCESS_PDB is the
thing of the future.

-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Frank
von Delft
Sent: Sunday, October 16, 2011 12:00 PM
To: [log in to unmask]
Subject: Re: [ccp4bb] IUCr committees, depositing images

One other question (for both key issues described):  what exactly is the
problem the committees are aiming to address?

Because I can't help noticing that Tom's email did not spark an on-list
discussion;  do people actually feel either are issues?  Isn't the more
burning problem how best to use the 10,000s of structures we're churning
out?  In the grand scheme of things, they're pretty inaccurate anyway:  
static snapshots of crippled fragments of proteins far from their many
interaction partners.  So do we need 100,000s of structures instead?  If so,
we may soon (collectively) stop being able to care about the original
dataset or how to reproduce analysis number 2238 from 2 years ago.

(No, I'm not convinced this question is relevant only to structural
genomics.)

phx.



On 16/10/2011 19:38, Frank von Delft wrote:
> On the deposition of raw data:
>
> I recommend to the committee that before it convenes again, every 
> member should go collect some data on a beamline with a Pilatus 
> detector [feel free to join us at Diamond].  Because by the probable 
> time any recommendations actually emerge, most beamlines will have one 
> of those (or similar), we'll be generating more data than the LHC, and 
> users will be happy just to have it integrated, never mind worry about 
> its fate.
>
> That's not an endorsement, btw, just an observation/prediction.
>
> phx.
>
>
>
>
> On 14/10/2011 23:56, Thomas C. Terwilliger wrote:
>> For those who have strong opinions on what data should be deposited...
>>
>> The IUCR is just starting a serious discussion of this subject. Two 
>> committees, the "Data Deposition Working Group", led by John 
>> Helliwell, and the Commission on Biological Macromolecules (chaired 
>> by Xiao-Dong
>> Su)
>> are working on this.
>>
>> Two key issues are (1) feasibility and importance of deposition of 
>> raw images and (2) deposition of sufficient information to fully 
>> reproduce the crystallographic analysis.
>>
>> I am on both committees and would be happy to hear your ideas 
>> (off-list).
>> I am sure the other members of the committees would welcome your 
>> thoughts as well.
>>
>> -Tom T
>>
>> Tom Terwilliger
>> [log in to unmask]
>>
>>
>>>> This is a follow up (or a digression) to James comparing test set 
>>>> to missing reflections.  I also heard this issue mentioned before 
>>>> but was always too lazy to actually pursue it.
>>>>
>>>> So.
>>>>
>>>> The role of the test set is to prevent overfitting.  Let's say I 
>>>> have the final model and I monitored the Rfree every step of the 
>>>> way and can conclude that there is no overfitting.  Should I do the 
>>>> final refinement against complete dataset?
>>>>
>>>> IMCO, I absolutely should.  The test set reflections contain 
>>>> information, and the "final" model is actually biased towards the 
>>>> working set.  Refining using all the data can only improve the 
>>>> accuracy of the model, if only slightly.
>>>>
>>>> The second question is practical.  Let's say I want to deposit the 
>>>> results of the refinement against the full dataset as my final model.
>>>> Should I not report the Rfree and instead insert a remark 
>>>> explaining the situation?  If I report the Rfree prior to the test 
>>>> set removal, it is certain that every validation tool will report a 
>>>> mismatch.  It does not seem that the PDB has a mechanism to deal 
>>>> with this.
>>>>
>>>> Cheers,
>>>>
>>>> Ed.
>>>>
>>>>
>>>>
>>>> --
>>>> Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
>>>>                                                  Julian, King of 
>>>> Lemurs
>>>>