[3dem] Prepare Depositions Using New pdb_extract Features
Justin Flatt
justin at rcsb.rutgers.edu
Fri May 12 07:28:31 PDT 2023
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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