RCSB PDB Mobile app FAQ

RCSB PDB Mobile is a new application for the Apple iOS platform (iPhone/iPod and iPad; an Android version is being developed). Search the entire PDB, view the latest weekly release of structures, access your MyPDB account, view the entire catalog of Molecule of the Month articles, and more using either a WiFi or cellular data connection. RCSB PDB Mobile is an update of the discontinued app PDBMobile.

Features of version 3.08 of the app include:

Information Access

• Molecule of the Month
• Latest news

Search & Lists

• Keyword searches
• Author searches
• PDB ID searches
• Personal annotation searches
• Save queries to MyPDB
• List all new entries
• List all annotated entries
• List all flagged entries
• The last five searches are listed on the results page

Visualization

• View structures from returned query results
• Enter individual structure PDB IDs

Query Results Browsing and Annotation

• View search results on single page
• View primary citation abstract (where available)
• Annotate entries
• Flag entries for later viewing/analysis

MyPDB Account Access & Management

• Stored query listing
• Stored query management
• Run MyPDB-stored queries

Context-sensitive integrated web browser access to the RCSB PDB website (iPad only)

• Open the web browser screen when viewing an entry to view full website information
• Perform website search and download results to the app's search listing
• View a selected molecule on the website interface within the apps molecular viewer

PDB File Association and Custom URL

• The app registers to handle .pdb text files from Email and Mobile Safari
• The app can be passed a link to PDB text file or PDB ID using the custom URL, e.g.:
  rcsbpdbmobile://7ENL
  rcsbpdbmobile://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=7ENL
  The custom URL can be used by other iOS apps or used within a web page opened in Mobile Safari.

Post structure record links to Facebook, Twitter and via email

• Post images directly from the molecular viewer screen
• Post links to your favorite Molecule of the Month

No. The main RCSB PDB website has the more comprehensive data presentation and search tools The utility of the RCSB PDB Mobile application is that it provides fast access to basic structure information on-the-go. It also provides you with a mobile connection to your MyPDB account and enables you to manage your MyPDB queries.

The RCSB PDB Mobile app is targeted at iOS devices (e.g. iPhone, iPod and iPad) running iOS version 5.1 or higher and Android version 2.3.3 or higher.

We are currently developing an Android version of the application, a beta version of which is available for download. We welcome your feedback regarding feature and platform requests for the RCSB PDB Mobile app.

The initial versions of the RCSB PDB Mobile app target the iPhone OS (iOS) and Android platforms because our website statistics indicate that devices using these operating systems account for the dominant proportion of mobile device access to the RCSB PDB website. Future version of the application may target other platforms. We welcome your feedback regarding feature and platform requests for the RCSB PDB Mobile app.

• iPhone, iPad and iPod Touch: Visit iTunes
• Android device: Beta version (version 2.3.3 and above)

The RCSB PDB Mobile app enables you to manage stored queries, add new queries and add personal annotations & flags.

Our initial work using HTML5 indicated this platform to be technically limited, particularly in respect to molecular visualization. The native application provides a very efficient means to access and visualize protein structures. Deployment through the (for example) Apple app store and (in future) the Android Market makes it easier for the RCSB PDB development team to push updates to end-users of the application in a timely fashion.

We currently do not store your MyPDB password in the app; future versions may include this feature.

Yes. The RCSB PDB Mobile app includes the NDKMol molecular viewer, developed by Dr Takanori Nakane of Kyoto University.
Display options for the viewer can be set either by clicking the "Settings" button in the Navigation bar or by enabling Speech Recognition in app settings.

Speech Recognition
Because of CPU requirements, it is recommended enabling this feature only in more recent iOS devices. Please give us feedback regarding whether you would like us to retain or enhance the speech recognition feature. Supported voice commands in the molecular viewer screen:

• "RENDER RIBBON"
• "RENDER STRAND"
• "RENDER C ALPHA TRACE"
• "RENDER B FACTOR TUBE"
• "RENDER NONE"
• "LIGAND SPHERE"
• "LIGAND STICK"
• "LIGAND LINE"
• "LIGAND OFF"
• "COLOR SPECTRUM"
• "COLOR CHAIN"
• "COLOR SECONDARY STRUCTURE"
• "COLOR POLARITY"
• "COLOR B FACTOR"
• "SIDE CHAIN ON"
• "SIDE CHAIN OFF"
• "DISPLAY ASYMMETRIC UNIT"
• "DISPLAY BIOLOGICAL ASSEMBLY"
• "DISPLAY CHAIN X" where "X" is the chain ID
• "HIDE CHAIN X" where "X" is the chain ID
• "HIDE ALL CHAINS"
• "DISPLAY ALL CHAINS"

Current limitations of implemented speech recognition:

• English language only recognized.
• "HIDE CHAIN" and "DISPLAY CHAIN" assignments are currently limited to upper case chain A through Z (the visibility of all chains can be set in the settings screen for the molecular viewer). Because of potential ambiguity in recognizing the chain IDs when spoken (for example "B" and "E" or "A and "K"), these two commands are probably the least reliable of the voice command set and should be used cautiously, enunciating the ID as clearly as possible.
• Works best in environments with very low ambient noise.

This feature uses the OpenEars shared-source iOS framework.

We are currently in the process of refactoring the RCSB PDB website to automatically accomodate different device form factors, including tablet devices.

Please let us know of any bugs you find by sending an email to info@rcsb.org including "Mobile feedback" in the subject line.

Yes, we welcome your feedback regarding feature and platform requests for our mobile applications.