Dear all,
The discussion about keeping primary data, and what level of data can
be considered 'primary', has - rather unsurprisingly - come up also in
areas other than structural biology.
An example is next generation sequencing. A full-dataset is a few tera
bytes, but post-processing
Dear Tassos,
It is unclear whether this thread will be able to resolve your deep
existential concerns about what to be, but you do introduce a couple of
interesting points: (1) raw data archiving in areas (of biology) other than
structural biology, and (2) archiving the samples rather than
Two senior structural biology positions available at AstraZeneca UK. One
is associate director of the crystallography/crystallization group
(recently mentioned in ccp4bb and still open) and has reference RD237,
the other is one position up and has just become available, the director
of protein
Still, after hundreds (?) of emails to this topic, I haven't seen any
convincing argument in favor of archiving data. The only convincing
arguments are against, and are from Gerard K and Tassos.
Why?
The question is not what to archive, but still why should we archive all
the data.
Because
Dear All,
As someone who recently left crystallography for sequencing, I
should modify Tassos's point...
A full data-set is a few terabytes, but post-processing
reduces it to sub-Gb size.
My experience from HiSeqs is that this full here means the
base calls - equivalent to the unmerged HKLs
I was hesitant to add my opinion so far because I'm used more to listen this
forum rather than tell others what I think.
Why and what to deposit are absolutely interconnected. Once you decide why
you want to do it, then you will probably know what will be the best format and
vice versa.
I have no doubt there are software developers out there who have spent
years building up their own personal collections of 'interesting' datasets,
file formats, and various oddities that they take with them wherever they
go, and consider this collection to be precious. Despite the fact that many
Dear Vaheh,
On Mon, Oct 31, 2011 at 03:18:07PM +, Oganesyan, Vaheh wrote:
But to store those difficult datasets to help the future software
development sounds really farfetched.
As far as I see the general plan, that would be a second stage (deposit
all datasets) - the first one would be
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
Dear Refmac users,
I noticed that if I refine a structure containing SeMet, then Se atoms usually
have big negative (red) peeks of difference map and high B-factors. As I
understand from the diffraction theory and from some discussions at CCP4bb,
that may result because in REFMAC the atomic
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
Pilot phase, opt-in--eventually, mandatory? Like structure factors?
Jacob
On Mon, Oct 31, 2011 at 11:29 AM, Adrian Goldman
adrian.gold...@helsinki.fi 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
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
Dear Adrian,
On Mon, Oct 31, 2011 at 06:29:50PM +0200, 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
The point is that science is not collecting stamps. Therefore the first
question should always be Why. If you start with What the discussion
immediately switches to technical issues like how many TB, PB etc.
$/EUR, manpower. And all the intense discussion will blow out by one
single Why.
Dear Martin,
Thank you for this very clear message about your views on this topic.
There is nothing like well articulated dissenting views to force a real
assessment of the initial arguments, and you have certainly provided that.
As your presentation is modular, I will interleave my
I would just model it with one water. Especially if resolution is worse than
1.8 (I dont think you have better based on the map)
Only if resolution is high and R-factors are low I would worry about this peak.
Regards,
Ivan
I believe that archiving original images for published data sets could be
very useful, if linked to the PDB.
I have downloaded SFs from the PDB to use for re-refinement of the
published model (if I think the electron density maps are misinterpreted)
and personally had a different interpretation of
Dear Martin,
First of all I would like to say that I regret having made my remark
500 and apologise if you read it as a personal one - I just saw it as an
example of a dataset it might have been useful to revisit if data had been
available in any form. I am sure that there are many skeletons
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