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
Weird. It's pretty much exactly what a nonbranched sugar (triose, in this
case) would look like.
were the dimensions consistent with three sugars? were there any collisions
with backbone or side chains inside/near the mystery density?
It really looks like maltotriose... is the protein a sugar bind
A few responses regarding TARDIS:
While it's true that TARDIS.edu.au is just an index to files hosted elsewhere,
a new solution, MyTARDIS has been developed as a repository that holds
information on diffraction (and other kinds of) data. The idea being that
facilities, labs or institutions take
Has anyone had problems with Refmac 5.6? I tried refining our stucture at 1.24
A,
aniso with H in riding position and it just exploded! I get error in distances
such as
Standard External All
Bonds: 3270 0 3270
Angles
Blob is gone--something funny happened, I guess. I went back to using
the original mtz from scala, removed and replaced a bunch of waters,
and no more worm! I can't really figure it out, and wish I knew
exactly what happened, but I think I am just going to non-chalantly
move along.
Jacob
On Thu,
Jacob,
By simply looking at the figures you show, it does look like you have some type
of long, maybe polymeric, molecule bound.
With that being said:
1- It is in the symmetry axis so maybe be a little noisy there
2-If you are in doubt about it being real or not check the density and how it
fits
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
Since this hasn't been brought up--there is the consideration that in
10 or more years maybe x-ray crystallography will be completely a
thing of the past, with some kind of massively-superior modality
taking over. Of course there is no way to bank on this, but I am
wondering whether this is somethi
Altering the thread title so " IUCr committees, depositing images" can be kept
on topic
George is right to raise the point about pixels not being read out at the same
time. In principle of course this could be corrected for. Although the Bruker
and PILATUS systems both allow shutterless operati
We store raw data for two main reasons:
a) We currently use only a fraction of the information actually contained in
raw images and extraction of that fraction can be improved. Destroying the data
means
- we lose the extra information, and make future research in some areas either
impossible o
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
Part of what is bothering me is that the density showed up at one
exact point in the refinement, and I am currently testing what exactly
it was that changed things. To me, the blob almost looks like a mask
of the molecule, and there is very little 2Fo density, so that's
weird. I am also really both
I agree with Rafael,
>From those pictures it looks like a sugar chain - maybe 2-3
saccharides in a row.
HTH
D
David C. Briggs PhD
Father, Structural Biologist and Sceptic
University of Manchester E-mail:
david.c.bri...@manchester.ac.uk
==
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
This is a reply to the group with a resolution of the frm2frm question. Frm2frm
is a utility program which is part of the Bruker PROTEUM suite of software. It
converts Bruker CCD frame images so they can be processed by external programs
eg MOSFLM.We can provide a demo copy of the software s
Hi, currently Refmac writes the wrong info for the low resolution
cutoff, for example:
REMARK 3 PROGRAM : REFMAC 5.6.0119
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.00
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 84.35
In contrast Shel-X
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
I think the key is that the questions asks "is a waste of money".
In a straightened funding time it may just be that storing the raw images in
addition to the processed
data doesn't float to the top of the list of "things that must be done whatever
else happens in science".
Something can be des
Maybe sugars?
El 10/27/11 6:27 PM, Jacob Keller escribió:
Dear Crystallographers,
In the course of a reasonably smooth refinement, all of a sudden there
is a huge worm-hole-type blob in the electron density (see pics). Has
anyone seen this before? Is it some effect of the refinement
over-fittin
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
On Thu, 2011-10-27 at 15:36 +0200, George M. Sheldrick wrote:
> In non-continuous mode, the goniometer has
> to accelerate at the start of a frame and decellerate at the end, then
> wait for
> the frame to be read.
Someone should be able to confirm this, but I was under impression that
at synchrot
Lots of systems go to 4C. Even a cheapo one like the Applied Biosystems
StepOnePlus.
-Morten Groftehauge
On 27 October 2011 03:17, Jürgen Bosch wrote:
> CD spec with Pelletier is an option too
>
> Jürgen
>
> ..
> Jürgen Bosch
> Johns Hopkins Bloomberg School of Public Health
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Jiyuan Ke,
the SSBOND
(http://www.ccp4.ac.uk/html/refmac5/files/coordinates.html#pdb_ssbond)
does allow symmetry related molecules, so it seems that is the header
entry you are looking for.
Tim
On 10/27/2011 03:56 PM, Ke, Jiyuan wrote:
> Dear A
Dear All,
I have a question regarding refinement of a crystal structure with
intermolecular disulfide bond. There is one monomer in an asymmetric unit. The
biological assembly for the molecule is a disulfide bond linked dimer. And the
disulfide bond is on a 2-fold crystallographic symmetry. Dur
There are two further complications. In non-continuous mode, the goniometer has
to accelerate at the start of a frame and decellerate at the end, then wait for
the frame to be read. So even if the shutter always functions perfectly, my
intuition tells me that it must be more accurate to rotate at
Dear Gerard,
Thankyou indeed for this clear and already detailed plan. As well as
for MX SR datasets, ~75% of the total, this plan can readily be
extended to eg SR SAXS and SANS.
For the benefit of CCP4bb participants just to mention that the IUCr
DDD WG is seeking 'can do' solutions across a bro
This discussion of image deposition and archival has certainly been
illuminating. While there have been clear directions on how the process would
actually work, I am becoming increasingly curious on why it should be done
(outside of threatening non publication, social acceptance, funding, etc).
Job opening for a structural biologist to join the “Biocrystallography
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A 2 year postdoctoral position with support from the French National
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Dear David,
As you probably have read in my previous message to Colin, I also agreed
with him.
I just wanted to clarify (and obviously not to him) what George said. It was
just a comment and not a lesson! Sorry if my message was misunderstood!
Martin
_
Dear all,
In response to my message below, posted yesterday afternoon (GMT+1) I
received an off-list message from John Helliwell asking me to clarify what I
had meant by "already stored information" when referring to the outline of a
feasibility study envisaged by the IUCr Forum. I answered
I agree with Colin here. Framing is simply a process of sampling an original
signal at some 'frequency' (related to the phi-width of each frame). At some
point, delta phi is small enough that the original signal is oversampled,
and can be reconstructed _within the bounds of noise_. Beyond that poin
Hi James,
1) thanks for sending and email in this thread longer than mine, I was
"worried" I had killed it... ;)
2) you say:
> 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 i
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Topic:
Structural characterization of protein complexes involved in the regulation
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Methods:
protein expression and
Dear Colin,
I think you understood perfectly what George was saying regarding the loss
of information, but he will probably answer better than I.
In any case, and for the ones that did not understand it, what George was
telling is related to the fact that a data collection made with a continuous
Hi,
This is why the right way to distribute *nix software is to distribute
> software itself and ask the end-user to get all the dependencies (not
> that hard these days).
it is a wonderful idea, apart from two tiny nuances: 1) many have no idea
about what the command line is, and 2) asking us
On Wednesday, 26 October 2011, James Holton wrote:
> 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/
>
Sorry Matt, some large facilities do already keep all their raw and processed
data. And I think the EU grant you mention to coordinate this is
http://www.pan-data.eu soon to be odi, includes the ESRF :), don't your
computing people tell you anything ?! :)
PanData have a meeting in early Novemb
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