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The policy doesn't say you can "supersede" someone else's entry.
It says you can deposit your own version, if you have a publication.
Then there will be two bogus structures instead of one. Pretty soon
the PDB will start to look like one of the cr
A little "loophole" that might make everyone happy can be found here:
http://www.wwpdb.org/policy.html
search for "A re-refined structure based on the data from a different
research group"
Apparently, anyone can supersede any PDB entry, even if they weren't the
original depositor. All they n
Exactly why I deposit the structure factors
Thank you PDB!!
On Wed, May 14, 2014 at 7:35 PM, Frances C. Bernstein <
f...@bernstein-plus-sons.com> wrote:
> From the earliest days the PDB accepted structure factor
> files along with coordinate files. If you check the early
> newsletters you will
From the earliest days the PDB accepted structure factor
files along with coordinate files. If you check the early
newsletters you will see that, unfortunately, most authors
did not deposit structure factor files. Eventually, as we
all know, deposition of structure factors became mandatory.
Th
Hello, I'm evaluating changes in crystal packing between different forms of my
protein. I use NCONT to calculate the number of atoms within a distance of 10 A
from each CA atom of the protein chain. My protein is also a crystallographic
dimer, then I want to list contacts between the two monomer
The Paul Scherrer Institute PSI is the largest research centre for
natural and engineering sciences within Switzerland. We perform
cutting-edge research in the fields of matter and materials, energy and
environment and human health. By performing fundamental and applied
research, we work on sus
Thank you! There is no exact definition of the reference zone in the
HKL2000 manual. Given a reciprocal lattice observed from one direction,
there may be several RotXYZs to reach it. It might be that the reference
zone is a sampling parallelogram from the real space used to determine the
orientatio
Dear Alastair,
As you point out, SHELXL allows atom names, RESIdue numbers and PARTs
(=Altlocs) to be used in any combination. The only rule is that no two
non-hydrogen atoms may have the same settings for all three. Other
refinement programs may be more restrictive.
Best wishes, George
On
thanks Tim. I have been using different "AltLoc" values (A,B) and
different "Atom name" values (HOH,CA) but the problem seems to be which
value to set for the "Residue name" field. Assigning different
residues numbers would seem to lose the distinction between partial and
alternate occupanc
On Wednesday, 14 May, 2014 13:52:02 Phil Jeffrey wrote:
> As long as it's just a Technical Comments section - an obvious concern
> would be the signal/noise in the comments themselves. I'm sure PDB
> would not relish having to moderate that lot.
>
> Alternatively PDB can overtly link to papers
Dear Alastair,
I think that refinement programs usually interpret chain ids A, B, ...
the way shelxl uses PART 1, 2, ... and a blank chain ID corresponds to
PART 0.
You may have to assign different residue numbers to CA and HOH, but I
think this is also the case for shelxl.
Does this resolve your
On Wed, May 14, 2014 at 10:53 AM, Mark Wilson wrote:
> As for the meaning of integrity, I'm using this word in place of others
> that
> might be considered more legally actionable. A franker conversation would
> likely more clearly draw the line that we're wrestling with here.
>
The reference t
Hi Nat,
I agree that journals should be doing the heavy lifting here, for the
reasons that you note. I also want to be clear that I believe the PDB is a
crowning achievement of transparency and open access in the sciences,
which is one reason that I am so concerned about this issue. I am in no
way
As long as it's just a Technical Comments section - an obvious concern
would be the signal/noise in the comments themselves. I'm sure PDB
would not relish having to moderate that lot.
Alternatively PDB can overtly link to papers that discuss technical
issues that reference the particular stru
On the subject of not (willfully) contaminating the pdb database, any
suggestions on the following are appreciated. I am refining the solvent
structure of some RNAs. Inspection of difference and anomalous
difference maps suggests that some closely-spaced positions are
alternately taken by dis
On Wed, May 14, 2014 at 10:26 AM, Mark Wilson wrote:
> Getting to Eric's point about an impasse, if the PDB will not claim the
> authority to safeguard the integrity of their holdings (as per their
> quoted statement in Bernhard's message below), then who can?
I think this may in part boil down
I vote for Z's idea
On Wed, May 14, 2014 at 12:32 PM, Zachary Wood wrote:
> Hello All,
>
> Instead of placing the additional burden of policing on the good people at
> the PDB, perhaps the entry page for each structure could contain a comments
> section. Then the community could point out serio
Hello All,
Instead of placing the additional burden of policing on the good people at the
PDB, perhaps the entry page for each structure could contain a comments
section. Then the community could point out serious concerns for the less
informed users. At least that will give users some warning
I think for questionable structures and those representing retracted paper, PDB
should be able to ask the depositors for raw data and leave it for the
community to decide if they still want to use the structure for science. If
the depositors can't or would not submit the data, it should be clea
Hi Tim,
Getting to Eric's point about an impasse, if the PDB will not claim the
authority to safeguard the integrity of their holdings (as per their
quoted statement in Bernhard's message below), then who can? I understand
that there are many potential complications to the PDB claiming some
plenar
I agree with Mark. The PDB should, at the very least, attach a warning label
to entries like 2HR0, where the scientific community has overwhelmingly
determined that the structure is invalid. In this case, I believe the author
never admitted any wrongdoing, and perhaps PDB policy prevents remov
Hi Mark,
I understand the discussion, yet as far as I understand the PDB does not
claim to be the authority to decide about the integrity of an entry (or
maybe better said, the PDB claims not to be this authority), and I find
it very honorable that the PDB have not abused their power. I don't mean
Hi Tim,
I agree with everything you've said about the importance of validation,
but aren't we really talking about something different here? Users of
structural information should of course be keeping a careful eye on
validation reports. On the other hand, what possible reason is there for
the PDB
Dear Eric,
On 05/14/2014 06:05 PM, Eric Williams wrote:
> [...]
> We seem to be at an impasse. The PDB won't evict highly suspect structure
> models unless journals retract them, and the journals in question have
> shown no indication of desiring to retract them. Is there anything that can
> be do
Hi James,
I am surprised the PDB contained any data at all at that time - wouldn't
people only submit their models but not the data at that time? ;-)
249GB and even the compressed 249GB data are not a 'tiny' space, as you
actually point out. At 'those days' I had three operating systems
installed
Dear all,
Following on from the CCP4BB posting about the release of update 15 we would
like to highlight a few points
about BLEND and encourage you to try it out should you have multi crystal data
that needs analysing:
1) the software needs the R package to be installed on your system. This is
Dear all,
a Ph.D. position in pharmaceutical and protein science is immediately available
in a pharmaceutical setting in collaboration with an academic chair of
interest.
The selected candidate will work with biomolecules of therapeutic relevance in
a highly modern environment at the interfac
Dear CCP4 users,
An update for the CCP4-6.4.0 series has just been released, consisting
of the following changes:
* BLEND: New program for optimum selection of multi-crystal datasets for merging
* Documentation: Help for BLEND
* CCP4i: BLEND interface and allow view of PNG files
* Examples: BLEND
The Worldwide Protein Data Bank (wwPDB) organization is proud to
announce that the Protein Data Bank archive now contains more than
100,000 entries.
Established in 1971, this central, public archive of
experimentally-determined protein and nucleic acid structures has
reached a critical milest
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