Frequently Asked Questions
regarding Depositing, Updating and Releasing
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Deposition, update and release policies
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What are the deposition and release policies?
Please view the current data deposition and release policies here.
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What types of biological structures are accepted by the PDB?
The wwPDB now accepts polypeptide structure depositions of all gene products; all naturally-occuring, non-ribosomally synthesized peptides, such as antibiotics; and all peptidic repeat units of larger polymers, such as fibrous and amyloid polymers. In addition, non-naturally occurring synthetic peptides with at least 24 residues will be accepted for deposition.
Consistent with earlier policy, depositions of polynucleotide and polysaccharide structures of 4 or more residues are also accepted. For more information, see the wwPDB Policy Guide at http://www.wwpdb.org/policy.html
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How do I submit X-ray, NMR, or EM structures to the PDB?
Each wwPDB member has tools for depositing data to the PDB archive.
To deposit your X-ray or EM structures with the RCSB PDB,
use our
ADIT deposition tool (or try ADITBeta!)
To deposit your NMR structures to the RCSB PDB/BMRB, use our ADIT-NMR tool.
Detailed instructions for
depositing structures solved by
X-ray crystallography,
NMR,
EM, and other methods are also available.
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Can I deposit a theoretical model to the PDB?
Since October 15, 2006, PDB depositions have been restricted to atomic coordinates that are substantially determined by experimental measurements on specimens containing biological macromolecules. This policy was recommended and endorsed by a working group comprised of structural and computational biologists and endorsed by the wwPDB advisory committee. Thus, theoretical model depositions (such as models determined purely in silico using, for example, homology or ab initio methods) are not accepted.
Theoretical models that have been previously released will continue to be publicly available via the existing models archive at ftp://ftp.wwpdb.org/pub/pdb/data/structures/models/current/.
A paper describing the outcome of the Workshop on Archiving Structural Models of Biological Macromolecules was published in Structure1.
1. H.M. Berman, S.K. Burley, W. Chiu, A. Sali, A. Adzhubei, P.E. Bourne, S.H. Bryant, J. Roland L. Dunbrack, K. Fidelis, J. Frank, A. Godzik, K. Henrick, A. Joachimiak, B. Heymann, D. Jones, J.L. Markley, J. Moult, G.T. Montelione, C. Orengo, M.G. Rossmann, B. Rost, H. Saibil, T. Schwede, D.M. Standley, and J.D. Westbrook (2006) Outcome of a workshop on archiving structural models of biological macromolecules. Structure. 14: 1211-1217.
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How do I replace coordinates (which I obtained as a result of re-refinement of my structure)?
We expect that before depositing your coordinates with the PDB,
you have completed your refinement. Re-refinement of the data
is not encouraged. In a few unusual scenarios (the referees of
your paper suggest a re-refinement, for example) you may send
revised coordinates to deposit@deposit.rcsb.org along with the
RCSB and PDB ID of the entry. As long as the entry has not
been released, it will be reprocessed with the new coordinates
and have the same RCSB and PDB ID. Please note that there will
be a delay in reprocessing the revised coordinates.
If the file has already been released, or if you collected new data after
the deposition of the original coordinate set, the new coordinates will
receive a new ID code and therefore should be deposited in a new ADIT
session. The original entry may remain in the archive in addition to
the new entry or be replaced by it. After you have completed deposition,
please send a message to deposit@deposit.rcsb.org alerting us that the
new entry should obsolete the earlier one. All citations will be carried over to the new entry.
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How do I replace my coordinates (which I obtained as
a result of collecting new data)?
The updated coordinates should be submitted as a new deposition
using ADIT to receive new PDB and RCSB IDs.
If the older deposition has already been released, you may either
choose to keep both the entries in the database or obsolete the
older entry. In the latter case, please e-mail the PDB and RCSB IDs
of the older entry to deposit@deposit.rcsb.org
explaining the
situation. The old entry will be obsoleted and linked to the new
deposition so that anyone searching for the old entry is
automatically directed to the new one. Initial citations will also be carried over into the new entry.
If the older deposition has not yet been released, it should be
withdrawn from the database. Please e-mail the PDB and RCSB IDs of
the older entry to
deposit@deposit.rcsb.org
with a request to
withdraw it and use the PDB ID of the new deposition in your
primary citation.
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During deposition, I made a mistake in typing my e-mail address
(or other information). How can I correct it?
Please send the correct e-mail address and any other
corrections regarding the deposition to deposit@deposit.rcsb.org
and include
the PDB and RCSB IDs of the entry in your
e-mail. The corrections will be incorporated in
your file by the annotation staff.
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I uploaded the wrong coordinate (or experimental data file)
during deposition. Can I replace it now?
If you uploaded the wrong file in your deposition session but
have not yet deposited your file, you should start a fresh
session with the correct file. The uploaded files can not be
replaced within a session, once it has been
started. Alternatively, you can complete your deposition and
send the correct file(s) to
deposit@deposit.rcsb.org
along with the RCSB and PDB IDs for the entry and a request to
replace the
file(s). The file(s) should be compressed (.Z or .gz) before
attaching to your e-mail.
If you realized that you have deposited the wrong file
immediately after deposition, you can again send the correct
file to deposit@deposit.rcsb.org and mention the RCSB and or
PDB ID for the entry. Please compress (.Z or .gz) the file(s)
before sending it via e-mail or FTP.
If this incorrect file has already been released, then follow the instructions as if you are replacing a new data set (two headings above).
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How can I deposit the experimental data for a structure that I
already deposited?
You can send the experimental data file to deposit@deposit.rcsb.org
with the PDB and or RCSB ID that it correspond
to. Please send the file in a compressed (.Z or
.gz) form. The experimental data will be included
in the deposition and released
appropriately.
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I am behind a firewall so I can not use the web version of
ADIT. How do I complete my deposition?
You can either use the validation server (web or
desktop versions) or the command line option for
validating the file that you prepared using pdb_extract or
the desktop version of
ADIT.
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How does an HPUB structure get released?
The HPUB status is used to indicate that a
structure will be released when the corresponding
journal article is published.
When we can confirm that the citation article
corresponding to a particular entry has been
released, the structure is included in the weekly
update of the PDB.
The PDB receives publication dates and citation
information directly from a few journals. For most
journals, however, the PDB scans the literature
for publication information. We also greatly appreciate
the citation information sent by anyone in the community to
deposit@wwpdb.org.
There is a one-year limit on the length of a
hold period, including HPUBs. If the citation for
a structure is not published within the one-year
period, depositors will be given the option to
either release or withdraw the deposition.
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Are sequence data available before release?
PDB depositors are given the opportunity to
prerelease a sequence in advance of the
coordinates. This decision is solely at the
discretion of the depositor, who may also choose to
hold the sequence information until the structure
is released.
The prerelease of sequence
data will allow users to conduct blind tests of
structure prediction and modeling techniques. It
could also help prevent unintended duplication of
effort in structure determination.
Sequence data are available before the release
of the corresponding coordinate data through the
PDB status search at http://www.pdb.org/pdb/search/searchStatus.do.
Users may query all available sequences, or query
based on criteria such as title or deposition date.
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What gets included in the Status Search?
The status search report shows the PDB ID,
expected release date (if available), deposition
date, citation title, entry authors, and release
status. If you need to suppress your title
information, please send a message to deposit@deposit.rcsb.org
after your structure has been deposited. Be sure to
include the RCSB ID for your entry. Please note
that the author list for the entry can not be
suppressed.
The macromolecular sequence(s) may be released
before the entry. Select "release now" from the
"Prerelease status for sequence information" menu
during deposition, and the sequence information
will appear in the status search after author
approval of the processed entry.
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What if I have a question about a released file?
Questions and changes about released files should be sent to
deposit@deposit.rcsb.org.
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Can a released structure be put back on hold?
Unfortunately, no.
Once an entry is released it may be
downloaded by any number of other sites, and data from
these sites cannot be recovered. For this reason, we ask that the files submitted for deposition are the finalized coordinates.
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How am I assigned a PDB ID? Can I request a particular ID?
As soon as you deposit your structure using ADIT,
your PDB ID will be displayed in the Web
browser.
Particular PDB IDs cannot be requested.
If you are behind a firewall and can not use the web
version of ADIT, you can send us your final,
validated coordinate and structure factor files via
e-mail
(deposit@deposit.rcsb.org) or
ftp (pdb.rutgers.edu). In such
instances, you should receive PDB and RCSB IDs for the
deposition within the next working day.
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Can a file be released without complete citation information?
Structures can be deposited, processed and released
without complete citation information. The journal
name, volume and page numbers can be sent to deposit@deposit.rcsb.org
when available. Please include the final title and
author list for the citation if it has changed
following deposition of the structure to the
PDB.
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Can I deposit a file to the Nucleic Acid Database?
Crystal structures of nucleic acids alone or nucleic
acids in complex with proteins are forwarded to the
Nucleic Acid Database (NDB) and
are assigned unique
NDB IDs either during the processing of the files or
after they have been released. NMR structures of
nucleic acids and their complexes are also forwarded
to the NDB. However, no unique NDB IDs are assigned
for NMR structures.
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Who is processing the data?
Structures deposited using ADIT are
processed immediately and returned to the author. The
files are fully processed and are released according
to the release status provided by the author. Data are
processed by the wwPDB annotators at the following locations:
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The RCSB PDB
Department of Chemistry
and Chemical Biology
Rutgers University
610 Taylor Road
Piscataway, NJ 08854-8087
732.445.0103 (phone)
732.445.4320 (fax)
deposit@deposit.rcsb.org
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PDBj
Institute for Protein Research
Osaka University
3-2 Yamadaoka, Suita-shi
Osaka 565-0871
Japan
81-6-6879-8634 (phone)
81-6-6879-8636 (fax)
adit@adit.protein.osaka-u.ac.jp
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PDBe
EMBL Outstation - Hinxton
Wellcome Trust Genome Campus
Hinxton
Cambridge, CB10 1SD
United Kingdom
44-(0)1223-494444 (phone)
44-(0)1223-494468 (fax)
pdbhelp@ebi.ac.uk
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What is the deadline for requesting release of entries?
PDB entries are processed by the members of the wwPDB (RCSB, PDBe and PDBj). They are either released when the corresponding paper is published (HPUB), released on a particular date (HOLD), or released immediately (REL).
Each week, all files scheduled for release or modification are checked and validated one final time. Authors may be contacted to resolve any issues that may arise while preparing the entries for release.
When the release of HPUB structures is requested, the PDB staff routinely confirms the primary citation. If this is not accomplished within that release cycle, the entry may be scheduled to be released in a later update.
To be included in the next update, any required author correspondence should be sent to the appropriate wwPDB member by noon Thursday (local time):
All entries due for release are transferred to the RCSB PDB for final packaging into the master PDB ftp archive. These files are then released at the target time of Wednesday 00:00 UTC (Coordinated Universal Time).
Requests received after these cutoff times will be processed during the next update cycle.
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How do I ...
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How do I FTP files to the PDB?
To ftp files (i.e., experimental data or
updated coordinates):
ftp pdb.rutgers.edu
user: anonymous
password: (your e-mail address)
cd private/adit
put (your files)
bye
Please e-mail the name of the files you uploaded to deposit@deposit.rcsb.org.
Please
also include the RCSB or PDB ID(s) of the entries these files
correspond with.
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How do I deposit a new chemical component (ligand)?
To deposit new ligands, please check Ligand Expo to see if the ligand, drug, ion, non-standard residue, modified residue, group, etc. is present in the Chemical Component Dictionary.
If the ligand is present, please make sure that the 3 letter code for the ligand in your file matches the one used in the Chemical Component Dictionary.
If the ligand is not present in the dictionary, depositors can upload a 2-D figure of the structure (e.g. PostScript, TIFF, or GIF) as part of theADITdeposition process. Coming soon, REFMAC/PHENIX users will be able to upload Monomer Sketcher Library files (*.cif format), for novel ligand deposition as well. From the left-hand categories menu, scroll down and select the "Upload Supplemental Information: Ligand Information" to provide this information. Although the 3 letter code used for the ligand has no specific significance, you may check Ligand Expo and select a code for your ligand that has not been taken; otherwise, one will be selected for you.
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How do I check the status of an unreleased file?
The RCSB PDB has developed a tool to search and create reports on
unreleased structures called
Status Search.
Questions and changes for unreleased
files should be sent to deposit@deposit.rcsb.org.
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ADIT
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What is ADIT?
ADIT, the AutoDep Input Tool, is used by the
community for the deposition and validation of data to
be included in the PDB archive. It is also used
internally by the RCSB PDB for data processing. To
deposit a structure, the user uploads the relevant
coordinate and experimental data files and adds
additional information using the ADIT editor. A
session ID number is provided for depositors who wish to
continue a deposition session at a later time. ADIT
is a Web-based tool that uses frames.
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Is there an ADIT tutorial?
A tutorial guide to using ADIT is available at
http://deposit.pdb.org/adit/docs/tutorial.html.
An ADIT tutorial in Japanese is at http://pdbdep.protein.osaka-u.ac.jp/tutorial_ja/.
Example "in progress" ADIT depositions are available at http://deposit-demo.rcsb.org
Instructions for depositing structures solved by
X-ray crystallography,
NMR, or
Electron Microscopy
using ADIT are available.
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Can I complete a
deposition over a few days? For how long is my
incomplete deposition session saved?
Yes, you can complete depositing a structure using
ADIT over a few
days.
In fact, your incomplete session is saved for a limit of 6 months from when it is first started.
When you start a session (for the first
time) it is assigned a session ID. The
session identifier appears in red in the center of the
browser window when the ADIT "deposit" step is first started. It
also appears in the title of the browser throughout the
deposition session. Save this and use it in the "Session
Restart ID" box when you access the session next
time. Restart IDs are case-sensitive. It should be entered
in the space provided on the ADIT home page to return to the
undeposited ADIT
entry. Once the deposition has been completed and
your entry has been assigned a PDB and RCSB ID, the
deposition session is not accessible.
ADIT stores the data entered in a category every time
the user presses the SAVE button. These data will be
available with the restart ID until the user deposits the
entry by selecting the "DEPOSIT NOW" button.
You may also prepare your structural data using the
desktop version of ADIT
and save data as mmCIF format files. This mmCIF
file can be reloaded into ADIT for editing, validation or
deposition.
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How can I base a new deposition on an older one?
At this time, a user can base a new entry on an
existing one by cutting the header from the older entry
and including it on top of the new coordinate file. This
new file becomes the input file to be uploaded into
ADIT. The ADIT editor can then be used to
modify the information in the file.
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I have 15 related
structures that I wish to deposit. What is the most efficient way
to deal with these depositions?
You can deposit one representative structure
following the instructions provided in the RCSB PDB
data deposition services in either PDB or mmCIF
format. Write to
deposit@deposit.rcsb.org
informing us about your 14 other related entries. Once
the first entry has been annotated, processed and
finalized, you can use this file as a template for your
subsequent depositions. In each case, replace the
coordinate section and update other information in the
file as necessary to prepare the files for
deposition.
You can deposit the remaining 14 files using ADIT (http://deposit.pdb.org/adit/,
or http://pdbdep.protein.osaka-u.ac.jp/adit)
or write to
deposit@deposit.rcsb.org
regarding depositing your files in batch mode. If these
depositions have ligands, drugs or inhibitors bound to
them, please check the Ligand
Expo and match the 3 letter code in the file to
the one used in the chemical component
dictionary. Otherwise please include detailed
information regarding the ligands and the entries they
are associated with to expedite the processing of these
files.
If these entries were solved using X-ray
crystallography, please use pdb_extract to prepare each
of these depositions. You can edit and complete all
the categories in the data template file for one of the
entries. Then cut and paste appropriate information
from here to complete all the other data template
files. This will eliminate repetitive typing of the
same information (like author name, citation
information, etc.) for all the depositions.
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I keep getting an error message – what could be wrong?
First try compressing the files that you are uploading,
either using compress or gzip (*.Z or *.gz).
An explanation of frequent file format problems is
available at http://deposit.pdb.org/validate/Validation_FAQ.html.
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How do I convert my structure factor file into mmCIF format?
We have created a structure factor file conversion tool for you, called sf-convert. The standalone version can be downloaded at http://sw-tools.pdb.org, or you can use the online version of sf-convert within our SF-Tool, a crystallographic data validation tool.
A tutorial for sf-convert is available as well.
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The citation for the entry has more than 10 authors,
but I only see 10 available boxes for the citation author
field. What should I do?
Fill out all the available boxes with the author
names, then save the frame by pressing on the save
button. Now go back to the same category "Citation
Authors" in the left hand frame of the ADIT
deposition page. When the frame is reloaded,
additional spaces will appear.
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How do I complete the sequence section in ADIT? How is this information represented in the PDB and mmCIF format files?
You must report the complete sequence that was used in the experiment including cloning artifacts, expression tags and residues that were not modeled due to missing density or constraints.
Then in ADIT, you should provide the best sequence database reference (e.g. UniProt, GenBank, etc., if available) in the Sequence section. The following points should be considered in selecting the reference sequence: The reference sequence should have the same source organism and gene form as that used in the experiment The sequence should also match perfectly barring any engineered mutations, residue modifications, cloning artifacts or expression tags. Any such conflicts should be clearly reported in the "Molecule details" section.
Sequence information is listed in the SEQRES records of the PDB format file and entity_poly section of the mmCIF file. The sequence database information forms the DBREF records (struct_ref and struct_ref_seq in mmCIF) while any discrepancies between the sequence in the database and that used for the structure solution are listed in the SEQADV section of the PDB format file (struct_ref_seq_dif in mmCIF).
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Validation Server
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What is validation? What is the ADIT Validation Server?
Validation is a means for checking the format
consistency, geometry and chemical interactions in your
structure compared to various standards. Close contacts
(within the asymmetric unit and between symmetry
related molecules), bond length, bond angle and torsion
angle deviations are reported. Incorrectly positioned
waters, chirality errors, sequence mismatches, missing
or extra atoms or residues are also highlighted.
The ADIT Validation Server reports geometrical and experimental checks using the programs NUCheck1,
PROCHECK2, and SFCHECK3. It should always be used prior to ADIT deposition, but can also be used independently of deposition to monitor improvements made to your structural model during the refinement process.
There are two versions of the ADIT
Validation Server available: the online versions can be found at http://deposit.pdb.org/validate/ and
http://pdbdep.protein.osaka-u.ac.jp/validate/.
The standalone version can be downloaded from http://sw-tools.pdb.org.
Tutorials are also available online at http://deposit.pdb.org/validate/docs/tutorial.html.
1Z.Feng, J. Westbrook, and H. M. Berman.(1998)
Rutgers University, New Brunswick, NJ
NDB-407. 2R.A. Laskowski, M.W. MacArthur,
D.S. Moss and J.M. Thornton. (1993). J. Appl. Cryst.,
26, 283-291. 3A.A. Vaguine, J. Richelle, and
S.J. Wodak. (1999). Acta Cryst. D55, 191-205.
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What is precheck?
In an ADIT session or in the
validation suite, when you upload new files to start a session, it is
recommended that you run precheck which quickly checks to see if the
file being uploaded has the correct format. It also extracts the
sequence of all polymers in the structure from the coordinates and
displays them by their one-letter code. This provides the user a
quick check to make sure that they have uploaded the correct file for
validation or deposition.
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I keep getting an error message – what could be wrong?
First try compressing the files that you are uploading,
either using compress or gzip (*.Z or *.gz).
An explanation of frequent file format problems
is available at
http://deposit.pdb.org/validate/Validation_FAQ.html.
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I think that my structure is correct. However, the
validation report shows that my structure has many
close contacts? What is going on?
Please check the unit cell dimensions and space
group included in the file during validation. Also, if
your PDB format file has a scale matrix (SCALE
records), please check to make sure that it is
correct. Any errors in these values can lead to several
close contacts in the validation report.
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I have a ligand in my structure that is ignored during
validation. What should I do?
Please check Ligand Expo
to see if the ligand in your structure is present in
our chemical
component dictionary. If the ligand is present,
please make sure that the 3 letter code that you have
used for the ligand matches that used in our
dictionary. Once you have updated your coordinate
file accordingly the ligand should be recognized
during validation.
If the ligand is not
present in the dictionary, proceed with the
validation and deposition of your structure. Based on
the information that you provide (chemical name,
formula, synonyms and a 2-D diagram), we will
check and add the ligand to our dictionary. During
the annotation of your file, the structure will be
validated. We will send you this report along with
the processed PDB file for your review.
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5 |
pdb_extract
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What does pdb_extract do?
pdb_extract can read in log files from
various crystallographic applications, coordinates and
structure factor files to automatically extract
relevant information regarding the data reduction,
scaling, heavy atom phasing, molecular replacement,
density modification and final structure
refinement. This program can combine all this
information to prepare a mmCIF format file for
validation and deposition to the PDB.
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What should I do if the program that I used for
solving the structure is not supported by pdb_extract?
If the program generates a coordinate file
in the PDB format and any log files in mmCIF
format, include these files and the name of the
program and pdb_extract should be able to prepare a
deposition file for you. Please send the name of
the unsupported program, any other relevant details
about it and its log file to
help@deposit.rcsb.org.
We will include this program
to our list of supported applications.
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I included all the appropriate file names for
running pdb_extract, but the program does not
run. What should I do?
Check the data template file to make sure
that there are no ‘????’ in the sequence
of the polymers. This represents a break in the chain
due to missing residues. Edit the sequence
information appropriately to ensure that all residues
that were not modeled due to missing density or
residues that were modeled as Ala or Gly due to
missing side chain density have been appropriately
corrected.
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All the residues in my coordinate file are
non-standard or modified. Will pdb_extract be able to
extract the sequence from the coordinate
file?
pdb_extract can recognize and extract the
sequence of polymers (protein or nucleic acid)
including some non-standard residues. The non-standard
or modified residues are denoted by their 3 letter
code as '(MSE)' for selenomethionine. However, if all
the residues in the polymer are non-standard,
the program may fail to get a correct register for the
sequence. Thus it is recommended that in such cases
the entity_poly (sequence) category should be manually
edited in the data_template.text file to ensure that
the sequence included is complete and correct.
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It will probably take me a long time to complete
solving this structure. Why should I bother with
pdb_extract right now?
pdb_extract can help you keep track of
all the relevant information from the different
stages of structure solution required for depositing
the structure. Apply pdb_extract to the
output and log files of each step of structure
determination (scaling, molecular replacement,
density modification etc.). Finally you can combine
all these output files (using the -icif
cif_file_name option) to generate an mmCIF format
file that contains all the information regarding the
different stages of structure solution.
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Questions, comments, and suggestions should be sent to
deposit@deposit.rcsb.org.
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Validation and Deposition Services Home
