We overestimate the value of individual structures because we're human :)
If a problem is important enough that one structure makes or breaks the
case, a sensible thing to do would be to get more structures and strive to
obtain some other flavor of pertinent information by methods that are
unlikel
On 17/10/2011 01:52, Wladek Minor wrote:
Frank,
This is serious problem for biologists. There is a structure with
ligand. The same data were re-interpreted and people did not find the
ligand. This re-interpretation is not really valid until we will look
into diffraction data. Biologist lost
Hi,
On Sun, Oct 16, 2011 at 7:48 PM, Ed Pozharski wrote:
> On Sat, 2011-10-15 at 11:48 +0300, Nicholas M Glykos wrote:
> > > > For structures with a small number of reflections, the
> > statistical
> > > > noise in the 5% sets can be very significant indeed. We have seen
> > > > differences betwe
On Sat, 2011-10-15 at 11:48 +0300, Nicholas M Glykos wrote:
> > > For structures with a small number of reflections, the
> statistical
> > > noise in the 5% sets can be very significant indeed. We have seen
> > > differences between Rfree values obtained from different sets
> reaching
> > > up t
I'm simultaneously embarrassed to have not read the thread to completion before
replying, and also totally pumped that I would answer a question the same way
as Bernhard Rupp!
On Oct 16, 2011, at 7:34 PM, Bernhard Rupp (Hofkristallrat a.D.) wrote:
> Ø Not if you are interested in scattering th
Ø Not if you are interested in scattering that falls between reciprocal
lattice maxima, or if you want to preserve the possibility of applying
future data reduction packages.
Yep, this is exactly what I expressed in my original statement:
diffuse solvent contributions, commensurate and
On Oct 16, 2011, at 4:18 PM, Bosch, Juergen wrote:
> The rest is comparable to a collection of stamps, although with the benefit
> as BR mentioned of adding an additional hurdle/layer to falsifying structures.
Not if you are interested in scattering that falls between reciprocal lattice
maxima
Ø Do you mean to reprocess determination of I and sig(I) from the
diffraction images automatically??? Or just to get an access to the raw
data?
Reprocessing the images with the to-be-developed new software that will
process the information in the data in full, and then using the
new-and-improv
On Oct 16, 2011, at 4:42 PM, Guenter Fritz wrote:
In the end for the determination of the structure only a few datasets
will be necessary. This means maybe 0.5 Tb of compressed data to
deposit. I don't think this is too much.
I think those 0.5 TB will be not essential, the more interesting data
On Oct 16, 2011, at 22:38 , Bernhard Rupp (Hofkristallrat a.D.) wrote:
> As in reprocess completely from images, I meant.
Do you mean to reprocess determination of I and sig(I) from the diffraction
images automatically???
Or just to get an access to the raw data?
FF
>
> From: Bosch, J
As in reprocess completely from images, I meant.
From: Bosch, Juergen [mailto:jubo...@jhsph.edu]
Sent: Sunday, October 16, 2011 1:31 PM
To: hofkristall...@gmail.com
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] IUCr committees, depositing images
Wasn't that already implemented in Phenix
On the technical feasibility of storage of original data:
Sure, running Pilatus for an olympic record, we will go home with several T of
data after 24 h (will we?).
Yes, we do already. I just checked the number of images from PILATUS 6M
we have collected so far this year : ca. 1.7 millions.
Wasn't that already implemented in Phenix ?
Jürgen
On Oct 16, 2011, at 4:20 PM, Bernhard Rupp (Hofkristallrat a.D.) wrote:
REPROCESS_PDB
..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins M
Dear all,
some current openings for PhD students, including those with interests in
structural biology:
13 PhD student positions at Biocenter Oulu for 2012-2015
http://www.biocenter.oulu.fi/bcogs_newpositions.html
plus a kind-of re-posting of my own ad:
---
A PhD student position (3 years, st
Hi Fellows,
I was attending the inaugural meeting of the Data Deposition Working Group
in Madrid. They are aware of the various points raised, and a
document/recommendation has been prepared that I assume will be soon made
public (John?). Amount of data seems not an insurmountable technical
proble
On the deposition of raw data:
Committees, wherever you are!
I guess that abstaining from storing the raw diffraction data in the form of
frames is not very wise
whatever its size is. I regret that for some PDB entries I do not have
diffraction data (needless to say that authors
do not submitted
One other question (for both key issues described): what exactly is the
problem the committees are aiming to address?
Because I can't help noticing that Tom's email did not spark an on-list
discussion; do people actually feel either are issues? Isn't the more
burning problem how best to use
On the deposition of raw data:
I recommend to the committee that before it convenes again, every member
should go collect some data on a beamline with a Pilatus detector [feel
free to join us at Diamond]. Because by the probable time any
recommendations actually emerge, most beamlines will ha
Hi Tommi :)
I like AKTA systems a lot, and it's uncharacteristic of me to say this but
the Micro is kind of a copout - it's a repurposing of the general AKTA
system towards smaller volumes and not a completely specific design like the
SMART was. Now, I think I understand why they're doing this --
Hi,
if you really want it SMART was replaced be Äkta Ettan and nowaays
Äkta micro. The nice thing is the easy of use (same software).
However i other think HPLCs might be more flexible and cheaper (e.g.
we have schimadzu - cant complain about anything,
interface is more complex, but you don
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