> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] raw data deposition
>
> On Oct 27, 2011, at 5:22 PM, Francis E Reyes wrote:
> > So I ask again, are there literature examples where reevaluation of the
> crystallographic data has directly resulted in new biological insights
into
On Friday, October 28, 2011 08:29:46 am Boaz Shaanan wrote:
> Besides, I thought that by now there are some standards on how data should
> be processed
> (this has been discussed on this BB once every few months, if I'm not
> mistaken).
If this is true, I must not have got the memo!
I hear
Dear Petr,
I agree that we need tools to validate processing methods, but these
tools will not come from pure thought alone: they will need vast amount of
raw data with a full range of problematic features so that the ideas of new
approaches and the algorithms to implement them can be develop
On Oct 27, 2011, at 11:56 PM, James Stroud wrote:
> This is a poor criterion on which to base any conclusions or decisions. We
> can blame the lack of examples on unavailability of the data.
Agreed. Reprocessing the data resulting in a a different biological result is
my personal reason and mo
I have said my piece of the issue of depositing but there is one comment I
would like to address.
Besides, I thought that by now there are some standards on how data should
> be processed (this has been discussed on this BB once every few months, if
> I'm not mistaken). Isn't that part of the vali
> E-mail: bshaa...@bgu.ac.il
> Phone: 972-8-647-2220 Skype: boaz.shaanan
> Fax: 972-8-647-2992 or 972-8-646-1710
>
>
>
>
>
>
> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Jacob Keller
> [j-kell...@fsm.northwestern.edu
92 or 972-8-646-1710
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Jacob Keller
[j-kell...@fsm.northwestern.edu]
Sent: Friday, October 28, 2011 5:05 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] raw data deposition
What about a case in which tw
Dear Jacob,
See the paper by J. Wang cited at the end of Francis Reyes's message
under this thread yesterday: it is a case of exactly what you are talking
about.
With best wishes,
Gerard.
--
On Fri, Oct 28, 2011 at 10:05:44AM -0500, Jacob Keller wrote:
> What about a c
Which trps protein check the MSGPP or SGPP website they might have what you are
looking for.
Jürgen
..
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street,
What about a case in which two investigators have differences about
what cutoff to apply to the data, for example, A thinks that Rsym of
50 should be used regardless of I/sig, and B thinks that I/sig of 2
and Rpim should be used. Usually A would cut off the data at a lower
resolution than B, especi
[CCP4BB@JISCMAIL.AC.UK] on behalf of Katherine
> Sippel [katherine.sip...@gmail.com]
> *Sent:* Friday, October 28, 2011 8:06 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] raw data deposition
>
> Generally during these rigorous bb debates I prefer to stay silent and
I must "say" that there were some emails exchanged between me and Gerard
later, in which I pointed out that I wasn't against deposition of images
(data frames). In fact, if SR sources kept user's data there would be
one more structure from here in the PDB: HDD failure here, the data on a
mirror
Dear Remy,
You are right, and I was about to send a message confessing that I had
been rash in my response to Fred's. Another person e-mailed me off-list to
point out that sometimes a structure can be quickly solved, but that doing
all the rest of the work involved in wrapping that structure
herine.sip...@gmail.com]
Sent: Friday, October 28, 2011 8:06 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] raw data deposition
Generally during these rigorous bb debates I prefer to stay silent and absorb all the information possible so that I can make an informed decision later on. I fear
Dear Fred,
Frankly, with respect, this sounds to me like fanciful and rather
non-sensical paranoia. The time frame for public disclosure of all SR data
has been quoted at 5 years, or something of that order. If someone has been
unable to solve a structure 5 years after having collected data o
D Bonsor wrote:
and allow someone else to have ago at solving the structure.
I'd be careful there if there was a motion to try to implement a policy
at SR sources (for academic research projects) to make it compulsory to
publically release all data frames after a period (1 year ? 2 years ?
Dear colleagues,
my opinion is that we should develop methods or approaches to validate
!processing! of raw data. If this is possible. We have many validation
tools for structure refinement, but no tool to validate data
processing. In case we have this tools, there is no need to deposit
diffractio
Generally during these rigorous bb debates I prefer to stay silent and
absorb all the information possible so that I can make an informed decision
later on. I fear that I am compelled to contribute in this instance. In
regards to the "does this make a difference in the biological interpretation
sta
On Oct 27, 2011, at 5:22 PM, Francis E Reyes wrote:
> So I ask again, are there literature examples where reevaluation of the
> crystallographic data has directly resulted in new biological insights into
> the system being modeled?
This is a poor criterion on which to base any conclusions or dec
Thanks for bringing this up front Ed. Specifically bringing your second point
to the forefront. Do we need to do it? Or to rephrase it more directly .. WHY
do we need to do it?
Answering why we need to do it will really help with compliance. Lest we not
forget we are asking the general crystal
Dear Adrian,
I too follow Voltaire, and your point of view nicely illustrates the
diversity of outlook and priorities between practitioners of our arcane art.
I can only say that I have seen many cases where structural detail only
obtainable through hard work in phasing and/or refinemen
Ok. This is my last post before I go to bed. Look at the opportunity cost of
this discussion alone - bright minds who should be solving structures or
developing algorithms - anything! Debating this.
However - as someone else remarked will (a) anyone care about > 90% of the
structures in 50 yea
Dear Nat,
You are making an excellent point, that I would like to supplement with
another drawn from an intermediate stage between making compulsory the
deposition of coordinates (to which you are referring) and the discussion we
are having right now about moving towards the deposition of dif
Every dataset costs money to produce. Is it more cost effective to expect that
those wishing to use the data repeat the expenditures by repeating the
experiments? To exaggerate the point, imagine a world without published
research articles, would it be more expensive to do science or less? We s
Dear Adrian,
thank you - this is most helpful in assessing why we do or don't need to
deposit the raw data.
However:
> And let me say that, as this bb hardly reaches ALL practicing MM
> crystallographers, but only those with an interest in techniques, the
> results AND discussion are heavily ske
ntry/dataset comes directly from the
> synchrotron facility during deposition so that users simply provide a unique
> dataset ID and the experimental details are pre-filled for them.
>
> Of course the above completely ignores home sources.
>
>
> /Michel
>> -----Origin
led for them.
Of course the above completely ignores home sources.
/Michel
> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of D
> Bonsor
> Sent: October-27-11 3:10 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] raw dat
Why should we store images?
There are many reasons why storing images can be useful, but one is the
ability to re-analyze the data for a structure, or for all structures, in
a systematic and improved way.
I imagine that in a few years the PDB-REDO approach to rebuilding
structures will be extende
This is my response to Gerard, originally off-list, but which he feels
needs to be made public.
Dear Gerard,
1. I think any opinion (collective or individual) by now is affected by
the ongoing discussion.
2. I am not sure how this would make the discussion less public.
3. Yes, we should contin
On Thu, Oct 27, 2011 at 1:47 PM, Adrian Goldman
wrote:
> 1) this is not a matter of science, but science (internal) policy, and so
> the majority actually SHOULD count.
>
It's worth keeping in mind that there was once strong opposition to the
current rules on PDB deposition - the best example I c
Why should we store images?
From most of the posts it seems to aid in software development. If that is the
case, there should be a Failed Protein Databank (FPDB) where people could
upload datasets which they cannot solve. This would aid software development
and allow someone else to have ago at
I strongly suspect that it is much more cost effective to have the PDB archive
a unit of data than it is to have it archived at the lab or department level.
So I suspect that more money will be available for doing science if we turn
over archival responsibilities for image data to the kind folk
Um, I have thought about entering this thread at least a dozen times. I've
started several comments and stopped all of them.
First, I am with the silent majority who doesn't think this data storage is a
good idea (or not a good enough idea) but who hasn't responded till now. And
let me say th
Sorry, the results in a pie-chart form are available here (but the
spreadsheet may be useful too if you want to see what is meant by
"other")
https://docs.google.com/spreadsheet/viewanalytics?hl=en_US&formkey=dHh4cjdLZGZrSEpUOG9kV2hkb3ZXNHc6MQ
--
Oh, suddenly throwing a giraffe into a volcano t
Dear Garib,
I am afraid clarification is in order.
Firstly, the results are available here
https://docs.google.com/spreadsheet/ccc?key=0Ahe0ET6Vsx-kdHh4cjdLZGZrSEpUOG9kV2hkb3ZXNHc
Click Form->Show summary to see the pie chart. This is so you don't
need to vote again to see the results (and ple
I never thought that science should be done democratically. (Note, I voted to
see results. Otherwise results are invisible). It would be unimaginable to
decide by majority vote that a particular equation or theory is valid (e.g.
relativity theory). I thought that storing data is a scientific
In medical school, I found out that there could be a large population
in a class which was completely lost or completely disagreed with what
was being said, but there was only silence. When the lecturer would
pose a question, it would take a painful silence before anyone in the
100+ student class w
Dear Jacob,
I agree, of course, with the goal of giving everyone a voice, but
knowing that 40% of the voters find storing images a waste of time falls
short of knowing why they think so and taking their arguments into account.
Disagreeing without saying why when a topic is being actively disc
On Thursday, October 27, 2011 09:30:20 am Jacob Keller wrote:
> One thing that the poll is useful for is something I find surprising:
> ~40% when I checked found storing images a waste of time. So, I guess
> this might be useful for finding the "silent [significant] minority."
> Why not have those
western.edu]
Sent: 27 October 2011 17:30
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] raw data deposition
One thing that the poll is useful for is something I find surprising:
~40% when I checked found storing images a waste of time. So, I guess
this might be useful for finding the "silent [si
One thing that the poll is useful for is something I find surprising:
~40% when I checked found storing images a waste of time. So, I guess
this might be useful for finding the "silent [significant] minority."
Why not have those folks chime in about why they think this is
useless, even to store ima
Dear Ed,
I am really puzzled by this initiative. It assumes that there is a
pre-formed "collective opinion" out there, independent from and unaffected
by the exchanges of views that have taken place on this BB, that would be
worth more than the conclusions we might reach by pursuing these exc
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