Step-by-step Instructions for using the pdb_extract webserver
pdb_extract can be used to convert PDB
format files to PDBx/mmCIF format and is a
vital resource for the submission of large
structures. You will be offered the option of
using a template file containing data that can
be shared among several depositions.
- Select one of the three methods
(X‐Ray, NMR, or EM).
Select the appropriate file type. Note:
PDB or mmCIF files can be used as input.
Browse to find the structure model coordinate file to
Click "Run" button to start PDB_extract
If your coordinate file has no
chain-IDs, pdb_extract will try to add by the best guess.
If pdb_extract detects any formatting
or data errors, it will stop and provide
error message. After they
are fixed, you can re-upload the file
If everything is ok after you click
the run button, you will get a second
webpage titled "Extracting Information for
PDB Deposition." This new page contains
various sections depending on the
- X-ray is fully supported for all of
the current crystallographic
applications including neutron and
X-ray/neutron hybrids. Pdb‐extract has a
data template file that can describe the
data collection. Log files can be processed to extract meta for data processing. The extracted data
will be combined with the templates and
merged into one model mmCIF
- The NMR option is
supported. A data template file (for the
author, and experiment conditions) is also
- The EM option is supported. A data
template file is available.
Press "Run" On the next page, a link
will be available for downloading the
extracted mmCIF format file
The file(s) are now ready for
deposition. To deposit the structure to the
wwPDB, please go to:
- "Information about Authors,
Detectors…" provides a template that can
be used for inserting various data items
into the extracted mmCIF file. This
is optional, as the information it
provides can also be entered via
the deposition interface.
- For X-ray structure, there are also
options to convert structure factors to
mmCIF format, extract information
from various steps of structure
determination and provide or verify the
unit cell parameters.
Information for PDB Deposition" page
provides macromolecular sequence
information that has been extracted from
the provided coordinate file. The
user can then review and edit each
sequence and its associated chain ID and
polymer type. Please note the following
- Sequence information extracted by
pdb_extract is automatically
read into the wwPDB Deposition System. It
is therefore important to correct all
issues with sequence at this stage.
- Missing, concatenated, or otherwise
unusual sequence information presented on
the “Extracting Information for PDB
Deposition” page may indicate the presence
of data or formatting errors in the
original coordinates that were not
directly detected by
pdb_extract. Please review
these sequences carefully.
- The extracted sequence information
should be corrected to include all
residues of each unique biopolymer,
including any unmodeled terminal regions
or gaps. Unobserved/missing residues should be included experimental sequence.