In the spirit of supporting a "can do" attitude, I have decided to try
and frame the binary "images or no images" question as a gradual scale.
Below is a list of ways to represent crystallographic data, with
increasing amounts of "information" as you move down. That is, making
validation more robust and allowing more and more yet-to-be-developed
technologies to be applied, but also requiring higher costs, such as
validation effort.
a) depositing coordinates only
b) coordinates and structure factors
c) coordinates, structure factors, and their sigmas (there was a time
when we didn't do this!)
d) scaled and merged intensities (before "truncate" or sqrt?)
e) scaled and "unmerged" intensities with combined partials (future
absorption corrections)
f) scaled spot intensities with partials separate (correct the shutter
jitter someday?)
g) unscaled individual spot intensities (with geometry for calculating
Lorentz, polarization, etc corrections)
h) spot intensities with a separate column for the "local background
level" (this would be an efficient way to "compress" the images)
i) spots, local background, and background levels partway between spots
(for reconstructing diffuse scatter)
j) all pixels from spot areas (~1000x compression over normal
"corrected" images)
k) spot pixels plus lossy compression of background (1000-30x over
corrected images)
l) losslessly compressed images (~2x over corrected images)
m) "corrected" images: all pixels from spatially-corrected
dark-and-flood applied images
n) uncorrected images with dark, flood and bad-pixel map for relevant
detector
o) raw output from detector's ADC or counter (no idea how to capture
this...)
p) cryo-preserved data crystal (for verification of cell, or just
chemical forensics, such as verifying the identity of the protein)
q) cryo-preserved duplicate crystal, to be held in a vault until you are
accused of fraud.
r) sample of pure protein with crystallization conditions
s) protein sequence, let the PDB "verify" the experiment by repeating
it, knowing that it "can be solved".
Now, I think it is clear that both the "benefit to the community" as
well as the burden on PDB resources increase as we move down this list.
In such situations one looks for "inflection points" where the next,
small increase in benefit requires a disproportionately large cost.
Historically, going from a to b was such an inflection point. This was
back when the compact disc was a new thing, and the whole PDB could fit
on one! In fact, if you had a "multi-session" drive you could back up
your hard drive onto the remaining space. Those days are gone.
Recently, I heard the PDB is seriously considering jumping to somewhere
between "e" and "g" (unmerged data). Doing so, I think, will be an
interesting exercise in file format "standardization" since every major
data processing package treats partials and postrefinement differently.
And this is perhaps the main reason why "the PDB" (aka Gerard K) are
wary of the idea of going all the way to "m" (corrected images). Do we
expect PDB staff to re-process our dataset as part of the "validation"
procedure?
Of course, if we are willing to relax the requirement of validation and
curation, this could be a whole lot easier. In fact, there is already
an image deposition infrastructure in place! It is called TARDIS:
http://tardis.edu.au/
Perhaps the best way forward would be for "the PDB" to introduce a new
field for one or more TARDIS ids in a PDB deposition? It would be
optional at the first, but no doubt required in the future.
-James Holton
MAD Scientist
On 10/26/2011 4:20 PM, Colin Nave wrote:
Dear Gerard
Yes, perhaps I was getting a bit carried away with the possibilities. Although I believe
that, with high resolution detectors and low divergence beams, one should be able to
separate out the various lattices it is not really relevant to the main issue - getting
the best from existing data. The point I made about "correcting" data probably
comes in a similar category - taking the opportunity to air a favourite subject.
Regards
Colin
PS. While here though I realise one of my points was a bit unclear. Point 5
should be
"5. My view is that for data in the PDB the same release rules should apply for the
images as for the other data. For data not (yet) in the PDB, the funders of the research
might want to define release rules. However, we can make suggestions!"
The original had "For other data" rather than "For data not (yet) in the PDB"
-----Original Message-----
From: Gerard Bricogne [mailto:g...@globalphasing.com]
Sent: 26 October 2011 23:23
To: Nave, Colin (DLSLtd,RAL,DIA)
Cc: ccp4bb
Subject: Re: [ccp4bb] IUCr committees, depositing images
Dear Colin,
Thank you for accepting the heavy burden of responsibility your
colleagues have thrown onto your shoulders ;-) . It is great that you are
entering this discussion, and I am grateful for the support you are bringing
to the notion of starting something at ground level and learning from it,
rather that staying in the realm of conjecture and axiomatics, or entering
the virility contest as to whose beamline will make raw data archiving most
impossible.
One small point, however, about your statement regarding multiple
lattices, that
"... all crystals are, to a greater or lesser extent, subject to this.
We just might not see it easily as the detector resolution or beam
divergence is inadequate. Just think we could have several structures
(one from each lattice) each with less disorder rather than just one
average structure."
I am not sure that what you describe in your last sentence is a realistic
prospect, nor that it would in any case constitute the main advantage of
better dealing with multiple lattices. The most important consequence of
their multiplicity is that their spots overlap and corrupt each other's
intensities, so that the main benefit of improved processing would be to
mitigate that mutual corruption, first by correctly flagging overlaps, then
by partially trying to resolve those overlaps internally as much as scaling
procedures will allow (one could call that "non-merohedral detwinning" - it
is done e.g. by small-molecule softeware), and finally by adapting
refinement protocols to recognise that they may have to refine against
measurements that are a mixture of several intensities, to a degree and
according to a pattern that varies from one observation to another (unlike
regular twinning).
Currently, if a "main" lattice can be identified and indexed, one tends
to integrate the spots it successfully indexes, and to abstain from worrying
about the accidental corruption of the resulting intensities by accidental
overlaps with spots of the other lattices (whose existence is promptly
forgotten). It is the undoing of that corruption that would bring the main
benefit, not the fact that one could see several variants of the structure
by fitting the data attached to the various lattices: that would be possible
only if overlaps were negligible. The prospects for improving electron
density maps by reprocessing raw images in the future are therefore
considerable for mainstream structures, not just as a way of perhaps teasing
interestingly different structures from each lattice in infrequent cases.
I apologise if I have laboured this point, but I am concerned that
every slight slip of the pen that makes the benefits of future reprocessing
look as if they will just contribute to splitting hairs does a disservice to
this crucial discussion (and hence, potentially, to the community) by
belittling the importance and urgency of the task.
With best wishes,
Gerard (B.)
--
On Wed, Oct 26, 2011 at 07:58:51PM +0000, Colin Nave wrote:
I have been nominated by the IUCr synchrotron commission (thanks colleagues!)
to represent them for this issue. However, at the moment, this is a personal
view.
1. For archiving "raw" diffraction image data for structures in the PDB, it
should be the responsibility of the worldwide PDB. They are by far the best place to do
it and as Jacob says the space requirements are trivial. Gerard K's negative statement at
CCP4-2010 sounds rather ex cathedra (in increasing order of influence/power do we have
the Pope, US president, the Bond Market and finally Gerard K?). Did he make the statement
in a formal presentation or in the bar? More seriously, I am sure he had good reasons
(e.g. PDB priorities) if he did make this statement. It would be nice if Gerard could
provide some explanation.
2. I agree with the "can do" attitude at Madrid as supported by Gerard B.
Setting up something as best one can with existing enthusiasts will get the ball rolling,
provide some immediate benefit and allow subsequent improvements.
3. Ideally the data to be deposited should include all stages e.g. raw images, "corrected"
images, MIR/SAD/MAD images, unmerged integrated intensities, scaled, merged etc. Plus the metadata,
software& versions used for the various stages. Worrying too much about all of this should not of
course prevent a start being made. (An aside. I put the "corrected" in quotes because the raw
images have fewer errors. The subsequent processing for detector distortions etc. depend on an
imperfect model for the detector. I don't like the phrase data correction).
4. Doing this for PDB depositions would then provide a basis for other data
which did not result in PDB depositions. There seems to be a view that the
archiving of this should be the responsibility of the synchrotrons which
generated the data. This should be possible for some synchrotrons (e.g.
Diamond) where there is pressure in any case from their funders to archive all
data generated at the facility. However not all synchrotrons will be able to do
this. There is also the issue of data collected at home sources. Presumably it
will require a few willing synchrotrons to pioneer this in a coordinated way.
Hopefully others will then follow. I don't think we can expect the PDB to
archive the 99.96% of the data which did not result in structures.
5. My view is that for data in the PDB the same release rules should apply for
the images as for the other data. For other data, the funders of the research
might want to define release rules. However, we can make suggestions!
6. Looking to the future, there is FEL data coming along, both single molecule
and nano-crystals (assuming the FEL delivers for these areas).
7. I agree with Gerard B - "as far as I see it, the highest future benefit of having
archived raw images will result from being able to reprocess datasets from samples
containing multiple lattices"
My view is that all crystals are, to a greater or lesser extent, subject to
this. We just might not see it easily as the detector resolution or beam
divergence is inadequate. Just think we could have several structures (one from
each lattice) each with less disorder rather than just one average structure.
Not sure whether Gloria's modulated structures would be as ubiquitous but her
argument is along the same lines.
Regards
Colin
-----Original Message-----
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Herbert
J. Bernstein
Sent: 26 October 2011 18:55
To: ccp4bb
Subject: Re: [ccp4bb] IUCr committees, depositing images
Dear Colleagues,
Gerard strikes a very useful note in pleading for a "can-do"
approach. Part of going from "can-do" to "actually-done"
is to make realistic estimates of the costs of "doing" and
then to adjust plans appropriately to do what can be afforded
now and to work towards doing as much of what remains undone
as has sufficient benefit to justify the costs.
We appear to be in a fortunate situation in which some
portion of the raw data behind a signficant portion of the
studies released in the PDB could probably be retained for some
significant period of time and be made available for further
analysis. It would seem wise to explore these possibilities
and try to optimize the approaches used -- e.g. to consider
moves towards well documented formats, and retention of critical
metadata with such data to help in future analysis.
Please do not let the perfect be the enemy of the good.
Regards,
Herbert
=====================================================
Herbert J. Bernstein, Professor of Computer Science
Dowling College, Kramer Science Center, KSC 121
Idle Hour Blvd, Oakdale, NY, 11769
+1-631-244-3035
y...@dowling.edu
=====================================================
On Wed, 26 Oct 2011, Gerard Bricogne wrote:
Dear John and colleagues,
There seem to be a set a centrifugal forces at play within this thread
that are distracting us from a sensible path of concrete action by throwing
decoys in every conceivable direction, e.g.
* "Pilatus detectors spew out such a volume of data that we can't
possibly archive it all" - does that mean that because the 5th generation of
Dectris detectors will be able to write one billion images a second and
catch every scattered photon individually, we should not try and archive
more information than is given by the current merged structure factor data?
That seems a complete failure of reasoning to me: there must be a sensible
form of raw data archiving that would stand between those two extremes and
would retain much more information that the current merged data but would
step back from the enormous degree of oversampling of the raw diffraction
pattern that the Pilatus and its successors are capable of.
* "It is all going to cost an awful lot of money, therefore we need a
team of grant writers to raise its hand and volunteer to apply for resources
from one or more funding agencies" - there again there is an avoidance of
the feasible by invocation of the impossible. The IUCr Forum already has an
outline of a feasibility study that would cost only a small amount of
joined-up thinking and book-keeping around already stored information, so
let us not use the inaccessibility of federal or EC funding as a scarecrow
to justify not even trying what is proposed there. And the idea that someone
needs to decide to stake his/her career on this undertaking seems totally
overblown.
Several people have already pointed out that the sets of images that
would need to be archived would be a very small subset of the bulk of
datasets that are being held on the storage systems of synchrotron sources.
What needs to be done, as already described, is to be able to refer to those
few datasets that gave rise to the integrated data against which deposited
structures were refined (or, in some cases, solved by experimental phasing),
to give them special status in terms of making them visible and accessible
on-line at the same time as the pdb entry itself (rather than after the
statutory 2-5 years that would apply to all the rest, probably in a more
off-line form), and to maintain that accessibility "for ever", with a link
from the pdb entry and perhaps from the associated publication. It seems
unlikely that this would involve the mobilisation of such large resources as
to require either a human sacrifice (of the poor person whose life would be
staked on this gamble) or writing a grant application, with the indefinite
postponement of action and the loss of motivation this would imply.
Coming back to the more technical issue of bloated datasets, it is a
scientific problem that must be amenable to rational analysis to decide on a
sensible form of compression of overly-verbose sets of thin-sliced, perhaps
low-exposure images that would already retain a large fraction, if not all,
of the extra information on which we would wish future improved versions of
processing programs to cut their teeth, for a long time to come. This
approach would seem preferable to stoking up irrational fears of not being
able to cope with the most exaggerated predictions of the volumes of data to
archive, and thus doing nothing at all.
I very much hope that the "can do" spirit that marked the final
discussions of the DDDWG (Diffraction Data Deposition Working Group) in
Madrid will emerge on top of all the counter-arguments that consist in
moving the goal posts to prove that the initial goal is unreachable.
With best wishes,
Gerard.
--
On Wed, Oct 26, 2011 at 02:18:25PM +0100, John R Helliwell wrote:
Dear Frank,
re 'who will write the grant?'.
This is not as easy as it sounds, would that it were!
There are two possible business plans:-
Option 1. Specifically for MX is the PDB as the first and foremost
candidate to seek such additional funds for full diffraction data
deposition for each future PDB deposiition entry. This business plan
possibility is best answered by PDB/EBI (eg Gerard Kleywegt has
answered this in the negative thus far at the CCP4 January 2010).
Option 2 The Journals that host the publications could add the cost to
the subscriber and/or the author according to their funding model. As
an example and as a start a draft business plan has been written by
one of us [JRH] for IUCr Acta Cryst E; this seemed attractive because
of its simpler 'author pays' financing. This proposed business plan is
now with IUCr Journals to digest and hopefully refine. Initial
indications are that Acta Cryst C would be perceived by IUCr Journals
as a better place to start considering this in detail, as it involves
fewer crystal structures than Acta E and would thus be more
manageable. The overall advantage of the responsibility being with
Journals as we see it is that it encourages such 'archiving of data
with literature' across all crystallography related techniques (single
crystal, SAXS, SANS, Electron crystallography etc) and fields
(Biology, Chemistry, Materials, Condensed Matter Physics etc) ie not
just one technique and field, although obviously biology is dear to
our hearts here in the CCP4bb.
Yours sincerely,
John and Tom
John Helliwell and Tom Terwilliger
On Wed, Oct 26, 2011 at 9:21 AM, Frank von Delft
<frank.vonde...@sgc.ox.ac.uk> wrote:
Since when has the cost of any project been limited by the cost of
hardware? Someone has to implement this -- and make a career out of it;
thunderingly absent from this thread has been the chorus of volunteers who
will write the grant.
phx
On 25/10/2011 21:10, Herbert J. Bernstein wrote:
To be fair to those concerned about cost, a more conservative estimate
from the NSF RDLM workshop last summer in Princeton is $1,000 to $3,000
per terabyte per year for long term storage allowing for overhead in
moderate-sized institutions such as the PDB. Larger entities, such
as Google are able to do it for much lower annual costs in the range of
$100 to $300 per terabyte per year. Indeed, if this becomes a serious
effort, one might wish to consider involving the large storage farm
businesses such as Google and Amazon. They might be willing to help
support science partially in exchange for eyeballs going to their sites.
Regards,
H. J. Bernstein
At 1:56 PM -0600 10/25/11, James Stroud wrote:
On Oct 24, 2011, at 3:56 PM, James Holton wrote:
The PDB only gets about 8000 depositions per year
Just to put this into dollars. If each dataset is about 17 GB in
size, then that's about 14 TB of storage that needs to come online
every year to store the raw data for every structure. A two second
search reveals that Newegg has a 3GB hitachi for $200. So that's
about $1000 / year of storage for the raw data behind PDB deposits.
James
--
Professor John R Helliwell DSc
--
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