On Friday, 06 February, 2015 13:38:14 Rachel Kramer Green wrote:
> Dear CCP4BB users,
>
> For additional information on this matter, please see:
>
> wwPDB Statement on Retraction of PDB Entries
> http://www.wwpdb.org/documentation/UAB.php
>
> and
>
> Safeguarding the integrity of protein archive
> /Nature/ (2010) *463*:425. doi:10.1038/463425c
> <http://www.nature.com/nature/journal/v463/n7280/full/463425c.html>
>
> Sincerely,
> Rachel Green
Both of those statements are now 5 years out of date.
The linked URLs at UAB are now dead.
The link to the US Office of Research Integrity works, but the
index to case summaries on that site has no listing for the Murthy affair
either as a closed or an open case investigation.
Furthermore the promised actions (retraction, obsolesence) apparently
never took place for whatever reason. Can you provide an update?
Do you think that an open letter from the community would be helpful?
Ethan
> On 2/6/2015 7:35 AM, Mark van Raaij wrote:
> > In our structures 1H6W (1.9Å) and 1OCY (1.5Å) we observed something
> > similar, I suspect the domain that makes the crystal contacts is
> > three-fold disordered, leading to layers of nothing. In our paper in
> > JMB 314, 1137 (doi 10.1006/jmbi.2000.5204) we tried to explain it a
> > bit, and describe what was done to try and "show up" the missing domain.
> >
> > The 2HR0 structure was clearly made up, as were the data, apparently
> > the mathematical function used to calculate the sigmas could be
> > derived from the deposited data...It is indeed a pity that neither the
> > structure nor the paper have been rejected. Perhaps the PDB is waiting
> > for Nature, and Nature for the PDB...a joint letter to both might be
> > in order to get this sorted out.
> >
> >
> > On 6 Feb 2015, at 11:58, Kerff Fred wrote:
> >
> >> Hello,
> >>
> >> Looking at structure 2HR0 ("The structure of complement C3b provides
> >> insights into complement activation and regulation. »,Abdul Ajees,
> >> A., Gunasekaran, K., Volanakis, J.E., Narayana, S.V., Kotwal,
> >> G.J., Krishna Murthy, H.M.; (2006) Nature 444: 221-225), I noticed
> >> the absence of contacts between layers in the crystal. Is it
> >> something that has already been observed in other crystals?
> >>
> >> Best regards,
> >>
> >> Fred
> >> -----
> >> Frédéric Kerff
> >> Chercheur qualifié F.R.S.-FNRS
> >> Cristallographie des protéines
> >> Centre d'Ingénierie des Protéines
> >> Université de Liège
> >> 17, Allée du 6 Août - Bat B5a
> >> 4000 Liège (Belgium)
> >> Tel.: +32 (0)4 3663620
> >> Fax: +32 (0)4 3663772
> >>
> >>
> >>
> >>> Le 6 févr. 2015 à 10:12, Tim Gruene <t...@shelx.uni-ac.gwdg.de
> >>> <mailto:t...@shelx.uni-ac.gwdg.de>> a écrit :
> >>>
> >>> -----BEGIN PGP SIGNED MESSAGE-----
> >>> Hash: SHA1
> >>>
> >>> Dear Smith,
> >>>
> >>> The sca file most likely does not contain flags. pointless can read
> >>> the sca file, standardise it to ccp4 standards and freerflag marks
> >>> random reflections. You should use the maximum of 500 unique
> >>> reflections or 5% of the unique reflections, whichever is larger.
> >>>
> >>> Best,
> >>> Tim
> >>>
> >>> On 02/06/2015 09:49 AM, Smith Lee wrote:
> >>>> Dear All, I have a sca file. Will you please tell me by which
> >>>> software or how I can know whether the sca file contains R-free
> >>>> tags? If not, by which software or how I can add the R-free tags?
> >>>> And how much of the reflections I add the R-free tags? I am looking
> >>>> forward to getting your reply. Smith
> >>>>
> >>>
> >>> - --
> >>> - --
> >>> Dr Tim Gruene
> >>> Institut fuer anorganische Chemie
> >>> Tammannstr. 4
> >>> D-37077 Goettingen
> >>>
> >>> GPG Key ID = A46BEE1A
> >>>
> >>> -----BEGIN PGP SIGNATURE-----
> >>> Version: GnuPG v1.4.12 (GNU/Linux)
> >>>
> >>> iD8DBQFU1IWVUxlJ7aRr7hoRAmZHAJ4+6wREnwkFN0EhfErAA0tPSopKKwCgiLdi
> >>> j0JFZac4kAh8twpov71MG84=
> >>> =XN57
> >>> -----END PGP SIGNATURE-----
> >
> > Mark J van Raaij
> > Lab 20B
> > Dpto de Estructura de Macromoleculas
> > Centro Nacional de Biotecnologia - CSIC
> > c/Darwin 3
> > E-28049 Madrid, Spain
> > tel. (+34) 91 585 4616
> > http://www.cnb.csic.es/~mjvanraaij <http://www.cnb.csic.es/%7Emjvanraaij>
> >
>
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
