Deposition of Half-maps for Certain EM Entries Now Mandatory

JY
Jasmine Young
Fri, Feb 25, 2022 3:25 PM

Dear pdb-l,

As announced previously
(https://www.wwpdb.org/news/news?year=2021#61afa92e5f450743ba4aa438),
deposition of half-maps for single-particle, single-particle-based
helical, and sub-tomogram averaging reconstructions to the EM Data Bank
(EMDB) is mandatory as of February 25, 2022. This change is in response
to a long-standing community request to the wwPDB EMDB Core Archive and
was also a recommendation from the 2020 wwPDB single-particle cryo-EM
data-management workshop (white paper in preparation). Several
recommendations from this workshop have already been implemented in the
wwPDB OneDep system. These include improvements to wwPDB validation
reports and enhancements for capturing metadata via the deposition
interface.

Mandatory half-maps must be unfiltered, unmasked, unsharpened, and
positioned in the same coordinate-space and orientation as the primary
map such that they superimpose. The availability of half-maps will
contribute to improved validation of EM structures as reflected in the
wwPDB validation reports.

wwPDB strongly urges developers of cryo-EM processing software for the
affected modalities to implement support for output of such half-maps
(if this is not already available).

Any queries about this policy change can be directed to info@wwpdb.org.

--
Regards,

Jasmine

---==========================
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email:jasmine@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320

---==========================

Dear pdb-l, As announced previously (https://www.wwpdb.org/news/news?year=2021#61afa92e5f450743ba4aa438), deposition of half-maps for single-particle, single-particle-based helical, and sub-tomogram averaging reconstructions to the EM Data Bank (EMDB) is mandatory as of February 25, 2022. This change is in response to a long-standing community request to the wwPDB EMDB Core Archive and was also a recommendation from the 2020 wwPDB single-particle cryo-EM data-management workshop (white paper in preparation). Several recommendations from this workshop have already been implemented in the wwPDB OneDep system. These include improvements to wwPDB validation reports and enhancements for capturing metadata via the deposition interface. Mandatory half-maps must be unfiltered, unmasked, unsharpened, and positioned in the same coordinate-space and orientation as the primary map such that they superimpose. The availability of half-maps will contribute to improved validation of EM structures as reflected in the wwPDB validation reports. wwPDB strongly urges developers of cryo-EM processing software for the affected modalities to implement support for output of such half-maps (if this is not already available). Any queries about this policy change can be directed to info@wwpdb.org. -- Regards, Jasmine =========================================================== Jasmine Young, Ph.D. Biocuration Team Lead RCSB Protein Data Bank Research Professor Institute for Quantitative Biomedicine Rutgers, The State University of New Jersey 174 Frelinghuysen Rd Piscataway, NJ 08854-8087 Email:jasmine@rcsb.rutgers.edu Phone: (848)445-0103 ext 4920 Fax: (732)445-4320 ===========================================================