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Improved Deposition for Cryo-Electron Microscopy

PDB deposition systems have been extended to accept data items specifically describing cryo-electron microscopy (cryo-EM) methods, for those EM methods that generate fitted coordinates. These items were developed in collaboration with members of the cryo-EM community, the EBI-MSD group, and the PDB.

New versions of ADIT (http://pdb.rutgers.edu/adit/ and http://pdbdep.protein.osaka-u.ac.jp/adit/) and AutoDep (http://autodep.ebi.ac.uk) that support these new data items for cryo-EM depositions are available.

Further information about AutoDep is available at http://autodep.ebi.ac.uk/autodep-doc/html/release-notes.html.

ADIT users can now select from the X-ray, NMR, or Cryo-EM deposition views. Further information about ADIT is available at http://pdb.rutgers.edu/.

Cryo-EM data item definitions are available from the following sources:

http://deposit.rcsb.org/mmcif/dictionaries/mmcif_iims.dic
http://deposit.rcsb.org/mmcif/dictionaries/mmcif_iims.dic/Index/
http://iims.ebi.ac.uk/iims_dictionary/iims.dic
http://iims.ebi.ac.uk/cif_iims.dic/Groups/em_group.html

A PDB file format template for REMARKs is available at:

http://iims.ebi.ac.uk/3dem_pdb.html
http://deposit.rcsb.org/cryo-em.html