POP-OUT | CLOSE

Frequently Asked Questions About this Website

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?

Almost all features of the RCSB PDB web site require a modern web browser with JavaScript and cookies enabled. To browse the database by exploring a hierarchy (for example, the taxonomy tree or the SCOP tree), pop-ups must not be blocked.

Supported Browsers
Here is a list of tested browsers grouped by desktop operating systems:

Mobile support
We currently offer limited support for browsing the site on a mobile device:

  • Android 2.1+
  • IPhone 3+
  • Learn more about our mobile app : PDBMobile

In addition, some functionality requires additional browser plug-ins:

Click here to check your browser compatibility for this website.

[+] 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):

http://www.rcsb.org/pdb/explore.do?structureId=4HHB

In addition, information on any PDB structure (experimental, theoretical, unreleased, or obsolete) may be retrieved with the following syntax (example 4HHB):

http://www.rcsb.org/pdb/search/structidSearch.do?structureId=4HHB

The syntax for linking to multiple PDB IDs on the site is as follows (example 1MI6, 1MVR):
(You can add as many PDB IDs as you like for the last parameter.)

http://www.rcsb.org/pdb/search/smart.do? smartSearchSubtype_1=StructureIdQuery&structureIdList_1=1MI6+1MVR

The older syntax of linking to the old production site (http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=4HHB) will be supported for a transition period. An announcement for the phasing out of this URL will be made on the homepage.

[+] What are the URLs to download files?

These syntaxes can be used to download files automatically:

http://www.rcsb.org/pdb/files/4hhb.pdb.gz
http://www.rcsb.org/pdb/download/downloadFile.do? fileFormat=xml&compression=NO&structureId=4HHB

Scripts are available to download multiple files from the FTP server.

[+] 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.

[+] Do you have a tutorial on how to use this site?

A overview of the RCSB PDB site is available at http://www.rcsb.org/pdb/static.do?p=general_information/getting_started/index.html.

A tutorial demonstrating how to use the Advanced Search is available at http://www.rcsb.org/pdb/static.do?p=help/advancedSearch.html.

Narrated screencasts demonstrate different features of the RCSB PDB website and tools, including Chemical Structure Search, widgets, and a tour of the left hand menu.

[+] 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 deposit@deposit.rcsb.org 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 http://www.rcsb.org/pdb/static.do?p=home/er.html.