RCSB PDB Data Validation and Deposition Services

Frequently Asked Questions regarding Depositing, Updating and Releasing Files

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1

Deposition, update and release policies

[+] What are the deposition and release policies?
[+] What types of biological structures are accepted by the PDB?
[+] How do I submit X-ray, NMR, or EM structures to the PDB?
[+] Can I deposit a theoretical model to the PDB?
[+] How do I replace coordinates (which I obtained as a result of re-refinement of my structure)?
[+] How do I replace my coordinates (which I obtained as a result of collecting new data)?
[+] During deposition, I made a mistake in typing my e-mail address (or other information). How can I correct it?
[+] I uploaded the wrong coordinate (or experimental data file) during deposition. Can I replace it now?
[+] How can I deposit the experimental data for a structure that I already deposited?
[+] I am behind a firewall so I can not use the web version of ADIT. How do I complete my deposition?
[+] How does an HPUB structure get released?
[+] Are sequence data available before release?
[+] What gets included in the Status Search?
[+] What if I have a question about a released file?
[+] Can a released structure be put back on hold?
[+] How am I assigned a PDB ID? Can I request a particular ID?
[+] Can a file be released without complete citation information?
[+] Can I deposit a file to the Nucleic Acid Database?
[+] Who is processing the data?
[+] What is the deadline for requesting release of entries?

2

How do I ...

[+] How do I FTP files to the PDB?
[+] How do I deposit a new chemical component (ligand)?
[+] How do I check the status of an unreleased file?

3

ADIT

[+] What is ADIT?
[+] Is there an ADIT tutorial?
[+] Can I complete a deposition over a few days? For how long is my incomplete deposition session saved?
[+] How can I base a new deposition on an older one?
[+] I have 15 related structures that I wish to deposit. What is the most efficient way to deal with these depositions?
[+] I keep getting an error message – what could be wrong?
[+] How do I convert my structure factor file into mmCIF format?
[+] 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?
[+] How do I complete the sequence section in ADIT? How is this information represented in the PDB and mmCIF format files?

4

Validation Server

[+] What is validation? What is the ADIT Validation Server?
[+] What is precheck?
[+] I keep getting an error message – what could be wrong?
[+] I think that my structure is correct. However, the validation report shows that my structure has many close contacts? What is going on?
[+] I have a ligand in my structure that is ignored during validation. What should I do?

5

pdb_extract

[+] What does pdb_extract do?
[+] What should I do if the program that I used for solving the structure is not supported by pdb_extract?
[+] I included all the appropriate file names for running pdb_extract, but the program does not run. What should I do?
[+] 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?
[+] It will probably take me a long time to complete solving this structure. Why should I bother with pdb_extract right now?
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Questions, comments, and suggestions should be sent to deposit@deposit.rcsb.org.