Dear Tassos,
If you apologise for a long e-mail in a long chain of them, I don't
know with what oratory precautions I should preface mine ... . I will
instead skip the disclaimers and try to remain brief.
It seems to me that there is a slight paradox, or inconsistency, in
your position. You concur with the view, expressed by many and just now
supported by George, that developers could perfectly well do their job on
the basis of relatively small collections of test datasets that they could
assemble through their own connections or initiative. I mostly agree with
this. So the improvements will take place, perhaps not to the same final
degree of robustness, but to a useful degree nevertheless. What would be
lost, however, is the possibility of reanalysing all other raw image
datasets to get the benefit of those new developments on the data associated
with the large number of other pdb entries for which they would have been
deposited if a scheme such as what has been proposed was put in place, but
will not have been otherwise.
Well and good, have said many, but who would do that anyway? And what
benefit would it bring? I understand the position of these sceptics, but I
do not see how you, dear Tassos, of all people, can be of this opinion, when
you have just in the previous sentence sung the praises of Gert and Robbie
and PDB-REDO, as well as expressed regret that this effort remains greatly
underappreciated. If at the time of discussing the deposition of structure
factor data people had used your argument (that it is enough for developers
to gather their own portfolio of test sets of such data from their friends
and collaborators) we could perhaps have witnessed comparable improvements
in refinement software, but there would have been no PDB-REDO because the
data for running it would simply not have been available! ;-) . Or do you
think the parallel does not apply?
One of the most surprising aspects of this overall discussion has been
the low value that seems to be given, in so many people's opinion, to that
possibility of being able to find improved results for pdb entries one would
return to after a while - as would be the case of a bottle of good wine that
would have matured in the cellar. OK, it can be a bit annoying to have to
accept that anyone could improve one's *own* results; but being able to find
better versions of a lot other people's structures would have had, I would
have thought, some value. From the perspective of your message, then, why
are the benefits of PDB-REDO so unique that PDB-REPROCESS would have no
chance of measuring up to them?
That is the best I managed to do to keep this reply brief :-) .
With best wishes,
Gerard.
--
On Tue, Nov 01, 2011 at 12:50:42PM +0100, Anastassis Perrakis wrote:
> Dear all,
>
> Apologies for a lengthy email in a lengthy chain of emails.
>
> I think Jacob did here a good job refocusing the question. I will try to
> answer it in a rather simplistic manner,
> but from the view point of somebody who might only have relatively little
> time in the field, but has enjoyed the
> privilege of seeing it both from the developer and from the user
> perspective, as well as from environments
> as the synchrotron service-oriented sites, as well as from a cancer
> hospital. I will only claim my weight=1 obviously,
> but I want to emphasize that where you stand influences your perspective.
>
> let me first present the background that shapes my views.
>
> <you can skip this>
>
> When we started with ARP/wARP (two decades for Victor and getting pretty
> close for myself!), we (like others) hardly
> had the benefit of large datasets. We had some friends that gladly donated
> their data to us to play with,
> and we have assembled enough data to aid our primitive efforts back then.
> The same holds true for many.
>
> At some point, around 2002, we started XtalDepot with Serge Cohen: the idea
> was to systematically collect phased data,
> moving one step away from HKL F/SigF to include either HLA/B/C/D or the
> search model for the molecular replacement solution.
> Despite several calls, that archive only acquired around hundred
> structures, and yesterday morning was taken off-line
> as it was not useful any more and was not visited by anyone any more. Very
> likely, our effort was redundant because of the JCSG
> dataset, which has been used by many and many people who are grateful for
> it (I guess the 'almost every talk' of Frank refers to me,
> I have never used the JCSG set).
>
> Lately, I am involved to the PDB_REDO project, who was pioneered by Gert
> Vriend and Robbie Joosten (who is now in my lab).
> Thanks to Gerard K. EDS clean-up and subsequent effort of both Robbie and
> Garib who made gadzillions of fixes to refmac,
> now we can not only make maps of PDB entries, but also refine them - all
> but less than 100 structures. That has costed a significant part of
> the last four-five years of Robbie's life (and has received limited
> appreciation from editors of 'important' journals and from referees of our
> grants).
>
> </you can skip this>
>
> These experiences are what shapes my view, and my train of thought goes
> like this:
>
> The PDB collected F/sigF, and to be able to really use them to get maps
> first, to re-refine later, and re-build now, has received rather
> limited attention. It starts to have impact to some fields, mostly to
> modeling efforts and unlike referee nr.3 I strongly believe it
> has a great potential for impact.
>
> My team collected also phases, so did JCSG in a more successful and
> consistent scale,
> and that effort has been used indeed by developers to deliver better
> benchmarking
> of many software (to my knowledge it has escaped my attention if anyone
> used JCSG data directly for eg by learning techniques,
> but I apologize if I have missed that). This benchmarking of software,
> based on 'real' maps for a rather limited set of data,
> hundreds and not tens of thousands, was important enough anyway.
>
> That leads me to conclude that archiving images is a good idea on a
> voluntary basis. Somebody who needs it should convince the funding bodies
> to make the money available, and then take the effort to make the
> infrastructure available. I would predict then 100-200 datasets would be
> collected,
> and that would really really help developers to make these important new
> algorithms and software we all need. Thats a modest investment,
> that can teach us a lot. One of the SG groups can make this effort and most
> of us would support it, myself included.
>
> Would such data help more than the developers? I doubt it. Is it important
> to make such a resource available to developers? Absolutely?
> What is the size of the resource needed? Limited to a few hundreds of
> datasets, that can be curated and stored on a modest budget.
>
> Talking about archiving in a PDB-scale might be fantastic in principle, but
> it would require time and resources to a scale that would not clearly stand
> the
> cost-benefit trial, especially at times of austerity.
>
> In contrast, a systematic effort of our community to deposit DNA in
> existing databanks like AddGene.com, and annotate PDB entries with such
> deposition
> numbers, would be cheap, efficient, and could have far-reaching
> implications for many people that could really get easily the DNA to start
> studying
> structures in the database. That would surely lead to new science, because
> people interested enough in these structures to claim the DNA and
> 'redo' the project would add new science. One can imagine even SG centers
> offering such a service 'please redo structure X for this and that reason',
> for a fee that would represent the real costs, that must be low given the
> investment already existing in experience and technology over there - a
> subset
> of targets could be on a 'request' basis...
>
> Sorry for getting wild ... we can of course now have a referendum to decide
> in the best curse of action! :-(
>
> A.
>
> PS Rob, you are of course right about sequencing costs, but I was only
> trying to paint the bigger picture...
>
>
>
> On Oct 31, 2011, at 18:00, Frank von Delft wrote:
>
>> "Loathe being forced to do things"? You mean, like being forced to use
>> programs developed by others at no cost to yourself?
>>
>> I'm in a bit of a time-warp here - how exactly do users think our
>> current suite of software got to be as astonishingly good as it is? 10
>> years ago people (non-developers) were saying exactly the same things -
>> yet almost every talk on phasing and auto-building that I've heard ends
>> up acknowledging the JCSG datasets.
>>
>> Must have been a waste of time then, I suppose.
>>
>> phx.
>>
>>
>>
>>
>> On 31/10/2011 16:29, Adrian Goldman wrote:
>>> I have no problem with this idea as an opt-in. However I loathe being
>>> forced to do things - for my own good or anyone else's. But unless I read
>>> the tenor of this discussion completely wrongly, opt-in is precisely what
>>> is not being proposed.
>>>
>>> Adrian Goldman
>>>
>>> Sent from my iPhone
>>>
>>> On 31 Oct 2011, at 18:02, Jacob Keller<[log in to unmask]>
>>> wrote:
>>>
>>>> Dear Crystallographers,
>>>>
>>>> I am sending this to try to start a thread which addresses only the
>>>> specific issue of whether to archive, at least as a start, images
>>>> corresponding to PDB-deposited structures. I believe there could be a
>>>> real consensus about the low cost and usefulness of this degree of
>>>> archiving, but the discussion keeps swinging around to all levels of
>>>> archiving, obfuscating who's for what and for what reason. What about
>>>> this level, alone? All of the accompanying info is already entered
>>>> into the PDB, so there would be no additional costs on that score.
>>>> There could just be a simple link, added to the "download files"
>>>> pulldown, which could say "go to image archive," or something along
>>>> those lines. Images would be pre-zipped, maybe even tarred, and people
>>>> could just download from there. What's so bad?
>>>>
>>>> The benefits are that sometimes there are structures in which
>>>> resolution cutoffs might be unreasonable, or perhaps there is some
>>>> potential radiation damage in the later frames that might be
>>>> deleterious to interpretations, or perhaps there are ugly features in
>>>> the images which are invisible or obscure in the statistics.
>>>>
>>>> In any case, it seems to me that this step would be pretty painless,
>>>> as it is merely an extension of the current system--just add a link to
>>>> the pulldown menu!
>>>>
>>>> Best Regards,
>>>>
>>>> Jacob Keller
>>>>
>>>> --
>>>> *******************************************
>>>> Jacob Pearson Keller
>>>> Northwestern University
>>>> Medical Scientist Training Program
>>>> email: [log in to unmask]
>>>> *******************************************
>>>>
>
> P please don't print this e-mail unless you really need to
> Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member
> Department of Biochemistry (B8)
> Netherlands Cancer Institute,
> Dept. B8, 1066 CX Amsterdam, The Netherlands
> Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791
--
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