Re: [ccp4bb] images

[Kay Diederichs]

Garib Murshudov schrieb:

Dear all

Before going into and trying to find a technical solution to the problem it would be good if decide if we need images. As far as I know if we face with a problem to solve and we know that it is necessary to solve then we find technical solution to the problem (either from other fields or we find our own solution with some elements of reinvention of new MX wheels). Do we need images to store? What kind of information we can extract from images that we cannot from amplitudes, intensities (even unmerged)? Does anybody have a convincing argument for favour of images?

Garib,









best,

Kay

I don't know if it convinces you or the community, but just a few days ago I was faced with the problem of finding out whether a bound cation in a PDB file deposited by others is a Mn or a Mg. The publication states Mn, the PDB file has a Mn, but I have reasons to suspect that it's actually a Mg. This obviously has some impact on the catalytic mechanism. In this case the structure factors were deposited, but these do not have a column for the anomalous signal. Re-refinement with these structure factors was inconclusive. If I could have downloaded the images, I could have investigated this easily, because there's a large difference in the f" of those two metals. So to me access to images sometimes may help to answer a scientific question.

regards
Garib



On 18 Mar 2009, at 16:32, Herbert J. Bernstein wrote:

Actually the radiologists who manage CT and PET scans of brains do have
a solution, called DICOM, see http://medical.nema.org/.  If we work
together as a community we should be able to do as well as the
rocket scientists and the brain surgeons' radiologists, perhaps even
better. -- 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, 18 Mar 2009, Jacob Keller wrote:

Apparently it DOES take a rocket scientist to solve this problem. Maybe the brain surgeons also have a solution?

JPK

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Northwestern University
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To: <CCP4BB@JISCMAIL.AC.UK>
Sent: Wednesday, March 18, 2009 5:36 AM
Subject: Re: [ccp4bb] images

----- Original Message ----- From: "Klaas Decanniere" <klaas.decanni...@vub.ac.be>

Herbert J. Bernstein wrote:

Have e.g. a look at http://heasarc.nasa.gov/docs/heasarc/fits.html
kind regards,
Klaas

Other sciences have struggled with this and seem to have found an answer.

 This is a good time to start a major crystallogrpahic image
archiving effort.  Money may well be available now that will not be
avialable six month from now, and we have good, if not perfect,
solutions available for many, if not all, of the technical issues
involved.  Is it really wise to let this opportunity pass us by?

The deposition of images would be possible providing some consistent
imagecif format was agreed.
This would of course be of great use to developers for certain
pathological cases, but not I suspect much value to the user
community - I down load structure factors all the time for test
purposes but I probably would not bother to go through the data
processing, and unless there were extensive notes associated with
each set of images I suspect it would be hard to reproduce sensible
results.

--
Kay Diederichs                 http://strucbio.biologie.uni-konstanz.de
email: kay.diederi...@uni-konstanz.de     Tel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universitaet Konstanz, Box M647, D-78457 Konstanz

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