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Does the PDB really renumber waters and ions before deposition? If yes,
than any reference in the paper to specific waters and ions might be
difficult/impossible to find in the deposited structure ... Usually, the
paper is written prior to deposition.
Dirk.
Eleanor Dodson wrote:
I dont like being told what to deposit, but on the other hand I am very
very grateful when I download a structure if the depositors have been
forced to follow a defined convention. (Note the recent correspondence
about Malenate)
It is up to us if we think the conventions are restrictive to make a
case for change - but please dont disregard them - we hope the
structures we deposit have some scientific interest to others, and the
users deserve consideration - I guess they represent the tax payers..
Eleanor
Gerard DVD Kleywegt wrote:
the guys at EBI always renumber the solvent molecules, ions and/or
ligands following a so-called uniformatory convention during
coordinate deposition.
i'm sure kim will respond and explain how this is done for a good reason
Would it be possible to make a lobby and get the PDB NOT TO CHANGE
anything we don�t want to have changed in the structures that are
supposed to be
alternatively - we could all follow the convention from the start
This is as if I went to the bank to deposit some money in what's
theore- tically my account and that it was actually the clerk that
told me how much I have to deposit !
since you need to deposit in order to publish (not to mention the fact
that most structures are paid for by tax-payers' money) i would argue
that the simile is wrong. it is more like going to the *tax office*.
and, yes, the tax man does tend to tell you how much you have to
deposit ... [of course, if you live in Natureland, Scienceland or
Cellland, you may get away with tax evasion ...]
--dvd
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Gerard J. Kleywegt
[Research Fellow of the Royal Swedish Academy of Sciences]
Dept. of Cell & Molecular Biology University of Uppsala
Biomedical Centre Box 596
SE-751 24 Uppsala SWEDEN
http://xray.bmc.uu.se/gerard/ mailto:[EMAIL PROTECTED]
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The opinions in this message are fictional. Any similarity
to actual opinions, living or dead, is purely coincidental.
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Dirk Kostrewa
Paul Scherrer Institut
Biomolecular Research, OFLC/110
CH-5232 Villigen PSI, Switzerland
Phone: +41-56-310-4722
Fax: +41-56-310-5288
E-mail: [EMAIL PROTECTED]
http://sb.web.psi.ch
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