Frequently Asked Questions

This page contains a number of frequently asked questions and answers. If this page does not address your questions, please visit our contact us page.

[+] What software do I need to take full advantage of the RCSB PDB website?

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[+] How do I link to a Structure Summary page for a PDB ID?

The correct syntax for linking to a Structure Summary page for a current experimental structure by PDB ID on the site is as follows (example 4HHB):
[+] What are the URLs to download files?

You can read all about this here.

[+] When downloading files, how do you use a gzipped(.gz) file?

A .gz file is a compressed file similar to a .zip. To open a .gz file, simply double click it to open it in your default archiving utility. If you do not have one, free programs like 7-Zip are available which will uncompress the file for you.

[+] When are new PDB entries released?

The PDB archive is updated each week on or about Wednesday 00:00 UTC (Coordinated Universal Time) with new entries, modified entries, and updated status information.

Updates are prepared on the previous Friday. Citation updates and release requests should be sent to by noon ET on the preceding Thursday to be included in an update; changes made after an update has been packaged will appear with the following update.

The files in the FTP archive have the Friday timestamp of the internal update packaging.

From the RCSB PDB site, the most recent release is timestamped and linked on every page from the top right header.

[+] How can I maintain a local copy of all PDB files?

Users can maintain their own local copy of all PDB files using rsync. Example scripts are available in the section on "Automated Download of Data from the RCSB PDB FTP Archive" on the FTP Services page.

Additional information on obtaining and maintaining copies of the entire PDB archive or certain portions of it is available from this README file in the FTP archive.

[+] What is PDB-101?

PDB-101 is a view of the RCSB PDB that places educational materials front and center. It packages together the resources of interest to teachers, students, and the general public to promote exploration in the world of proteins and nucleic acids.

Clicking on the blackboard PDB-101 logo or its related widget in the left-hand menu takes the user to PDB-101. This view offers easy navigation: select any Molecule of the Month article from the top bar menu or mouse over the PDB-101 pulldown to jump to other sections of PDB-101. Click on the blue logo in the top left at any time to access RCSB PDB deposition and query services from the main website.

Each Molecule of the Month highlights specific PDB entries. These "Discussed Structures" have their own PDB-101 Structure Focus page.

[+] What external data does the RCSB PDB website use?

The RCSB PDB combines the primary data from PDB archival files with data from external resources to enhance the query and display functionality on the RCSB PDB website. A listing of such external data is provided in the table at external resources page.