[3dem] Prepare Depositions Using New pdb_extract Features

[Justin Flatt]

pdb_extract merges coordinate data, author-provided metadata, and data 
processing information from output files produced by structure 
determination programs into a complete PDBx/mmCIF file that can used for 
easy deposition with OneDep. Use the pdb_extract online form [1] or the 
easily-installed command line interface [2] that been re-engineered 
(Python).

COORDINATE DATA

Uploaded coordinate files (PDBx/mmCIF or PDB) will be checked against 
the PDBx/mmCIF dictionary. Legacy PDB formatted files will be converted 
to a OneDep-compliant PDBx/mmCIF data file.

METADATA

Depositors are encouraged to use the PDBj CIF editor to easily edit a 
template file to include corresponding metadata (sequence, 
crystallization condition, etc.). Method-specific templates have been 
pre-loaded into the PDBj CIF editor: X-ray [3], 3DEM [4], and NMR [5]. 
Click on the top-left menu (light gray widget icon) to save the edited 
metadata file in PDBx/mmCIF. Upload this completed file in pdb_extract 
to prepare single or multiple related structures for submission.

STRUCTURE DETERMINATION OUTPUT FILES

Upload the log file produced during data processing, and pdb_extract 
will parse the related diffraction metadata. Log files from various 
standalone packages and from CCP4 and autoPROC pipelines are supported, 
including:

  	* Aimless
  	* DIALS
  	* d*TREK
  	* HKL-2000
  	* HKL-3000
  	* Pointless
  	* Scala
  	* Scalepack
  	* XDS
  	* Xia2
  	* Xscale



Links:
------
[1] https://urldefense.com/v3/__https://pdb-extract.wwpdb.org/__;!!Mih3wA!HUdhHKvs8sVjyRJylWRHUH5mUQzRYo11AaamOXRINDyZ-h4oPKG3-kbyi9OJQYH9LtBGoEuppkOGr9iAolku1hrS$ 
[2] https://urldefense.com/v3/__https://sw-tools.rcsb.org/apps/PDB_EXTRACT/source.html__;!!Mih3wA!HUdhHKvs8sVjyRJylWRHUH5mUQzRYo11AaamOXRINDyZ-h4oPKG3-kbyi9OJQYH9LtBGoEuppkOGr9iAoiBgxW6N$ 
[3] 
https://urldefense.com/v3/__https://pdbj.org/cif-editor/*filterErroneousData=false,url=https:/*pdb-extract.wwpdb.org/help/data_template_xray.cif__;Iy8!!Mih3wA!HUdhHKvs8sVjyRJylWRHUH5mUQzRYo11AaamOXRINDyZ-h4oPKG3-kbyi9OJQYH9LtBGoEuppkOGr9iAorqZyVdW$ 
[4] 
https://urldefense.com/v3/__https://pdbj.org/cif-editor/*filterErroneousData=false,url=https:/*pdb-extract.wwpdb.org/help/data_template_em.cif__;Iy8!!Mih3wA!HUdhHKvs8sVjyRJylWRHUH5mUQzRYo11AaamOXRINDyZ-h4oPKG3-kbyi9OJQYH9LtBGoEuppkOGr9iAonnvEVY5$ 
[5] 
https://urldefense.com/v3/__https://pdbj.org/cif-editor/*filterErroneousData=false,url=https:/*pdb-extract.wwpdb.org/help/data_template_nmr.cif__;Iy8!!Mih3wA!HUdhHKvs8sVjyRJylWRHUH5mUQzRYo11AaamOXRINDyZ-h4oPKG3-kbyi9OJQYH9LtBGoEuppkOGr9iAouIK9cg-$ 
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