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May 9, 2012

Data Download in Visualizations

We have released a new version of the DEVise visualization tool that allows users to download data from a given view within a visualization.

To download data from a view, select data download mode in the toolbar (the icon). Then click in the view for which you want to download the data. Your browser should create a new tab or window with a comma-separated value file containing the data, which you can then save to your computer. (If your browser does not create such a tab or window, you can manually copy and paste the URL from the DEVise dialog into a browser tab or window.)

Note that some visualizations have multiple views overlaid on each other, with a transparent background for all but the back view. In this case, if you download data, you will get data for each view that is overlaid (all in a single file, but with each data set separated by header information).

Currently, only data falling within the axis ranges of the view as it's currently displayed is downloaded. Therefore, if you want to be sure to get all data associated with the view, do home ( in the toolbar) on the view before doing your data download.

This feature works with all visualizations (single-entry, two-entry, histograms, and the visualization server). The main limitation is that it currently does not work in three-dimensional views. (It does, however, work in the two-dimensional view of visualizations containing three-dimensional views.)

May 31, 2011

S2 Predicted vs. Experimental Visualizations

We have added visualizations of S2 predicted vs. experimental values to the available visualizations for BMRB entries. (Predicted values are determined from the relevant PDB structure by s2predict.)

S2 predicted vs. experimental visualizations are currently available for the following entries:

For entries for which this visualization is available, you can view it by simply selecting the appropriate link in the visualization summary page.

March 14, 2011

Two-Entry Visualizations

We have released a new version of the Peptide-CGI visualization generation tool that allows the creation of visualizations incorporating data from two entries (or data uploaded to the visualization server and a released entry). At the present time, the two-entry visualizations available are the simulated 1H-15N backbone HSQC spectrum and the simulated 1H-13C HSQC spectrum (more visualizations are planned). It is not yet possible to generate visualizations combining two visualization server data sets.

You can access the two-entry visualizations in two ways:

On the visualization summary page for each entry (or visualization server data set), there is a form that allows you to enter an accession number, which is then visualized in combination with the current entry.
There is also a two-entry selection page.

Note that, to compare uploaded data with a released entry, you must first upload your data to the visualization server and generate the single-data set visualizations. At that point, you can specify an entry to compare with your data.

For an example using entries 16606 and 16607, click here.

July 12, 2010

Visualizations of distance restraints and their violations

We have added visualizations of distance restraints to the available visualizations for BMRB entries. The visualizations consist of distance restraint data (from the restraints grid, with violations calculated by CING, or from the remediated restraints), combined with coordinates from the PDB entry, producing integrated visualizations of the distance restraint data and the 3D structure. The distance restraint data can also be visualized based on PDB ID, rather than BMRB accession number (see the BMRB search page at http://www.bmrb.wisc.edu/search/).

For more detailed information, see the visualization help page here.

July 9, 2010

NMR derived binding data now archived in BMRB entries

BMRB entries containing binding constants (Kd) and reaction rate constants (kon and koff) extracted from the peer-reviewed literature are now being released to the public. A link, Binding Data, on the BMRB homepage provides access to a webpage with the full list of entries and links to individual entries. NMR spectroscopists, who are publishing these kinds of data, are strongly encouraged to deposit their results at BMRB.

April 29, 2010

Combined chemical shifts - remediated restraints - coordinates files released on the FTP site

We have released 400+ files that combine BMRB NMR data with remediated restraints and PDB coordinates. The files are located in /pub/bmrb/nmr_pdb_integrated_data/coordinates_restraints_chemshifts/bmrb_plus_pdb directory on the BMRB FTP site and are also accessible via HTTP URL.

Files are named merged_BMRB-ID_PDB-ID.str and entry IDs in the files follow the pattern: cBMRB-ID_PDB-ID. For example, the file merged_10141_2e9g.str combines data from BMRB entry 10141 and PDB entry 2e2g, and has internal entry ID c10141_2e2g.

February 3, 2010

Torsion angle restraint visualizations

We have added visualizations of torsion angle restraints, and their violations, to the available visualizations for BMRB entries. The visualizations consist of torsion angle restraint data (from the restraints grid, with violations calculated by CING), combined with coordinates from the PDB entry, producing integrated visualizations of the torsion angle restraint data and the 3D molecule. The torsion angle data can also be visualized based on PDB ID, rather than BMRB accession number (see the search page). For more detailed information, see the visualization help page.

December 21, 2009

We have added a CS-Rosetta structure calculation service to the BMRB website. Users can upload chemical shift files and run the protein structure prediction software CS-Rosetta on a CONDOR high-throughput computing cluster.

December 8, 2009

Visualization tutorial videos

We have developed two tutorial videos on the use of the DEVise/JavaScreen web-based visualization tool at the BioMagResBank web site. The subjects of the tutorials are as follows:

Tutorial 1 covers DEVise cursors, zooming, the most important toolbar modes (drill down, cursor fill, home, and view help), accessing the JavaScreen help page, and how to access visualizations at BMRB.

Tutorial 2 covers the BMRB visualization summary page for each entry, the rest of the toolbar modes (zoom modes, axis range toggle, and symbol enlarge/reduce), and session restart, axis range reset, display (color) modes, and communication modes (normal and CGI).

We hope that these tutorials will make it easier for users to fully take advantage of the capabilities of the JavaScreen visualization tool.

We plan to create more tutorials, covering topics such as the 3D interface in the JavaScreen and the use of the visualization server at BMRB.

URLs for the videos are below:

Tutorial 1, main youtube page: http://www.youtube.com/watch?v=OoYRIMIi7_g

Tutorial 1, embedded:

Tutorial 2, main youtube page: http://www.youtube.com/watch?v=94_hy770aQU

Tutorial 2, embedded:

October 2, 2009

NMR-STAR files available via REST API

BMRB entries can now be retrieved from the following URLs:

http://rest.bmrb.wisc.edu/bmrb/Entry_ID/html returns HTML summary page for BMRB entry Entry_ID. For example, http://rest.bmrb.wisc.edu/bmrb/10001/html
http://rest.bmrb.wisc.edu/bmrb/Entry_ID/nmr-star3 returns BMRB entry Entry_ID in NMR-STAR 3.1 format. For example, http://rest.bmrb.wisc.edu/bmrb/10001/nmr-star3
http://rest.bmrb.wisc.edu/bmrb/Entry_ID/nmr-star2 returns BMRB entry Entry_ID in NMR-STAR 2.1 format. For example, http://rest.bmrb.wisc.edu/bmrb/10001/nmr-star2

July 30, 2009

Time domain data links inserted into BMRB NMR-STAR files

Links to time domain data have been incorporated into the NMR-STAR v3.1 files for 106 BMRB entries (ftp://ftp.bmrb.wisc.edu/pub/bmrb/timedomain_entries/). This includes links to the raw spectral data that was processed and analyzed to produce assigned chemical shifts and constraints for structure calculations. Links for pulse programs, acquisition parameters, processing parameters, and peak lists are also included in the entries for many NMR experiments. This information can be used to develop new methods of automatic structure calculation, peak assignment, and analysis.

June 1, 2009

New page for pre-deposition validation tools

There is now a new page on the BMRB web site highlighting the various validation tools that can be used by depositors. This page was created in response to requests that validation tools be more accesible to depositors. The BMRB strongly encourages pre-deposition validation of NMR experimental data and structure files.

December 19, 2008

Ambiguity code assignment interface

A web-based program for assigning chemical shift ambiguity codes is available in the Deposit section of BMRB website. The program finds potentially ambiguous chemical shift assignments in an NMR-STAR 3.1 table and asks which are unique. The output is an NMR-STAR 3.1 table with ambiguity codes filled in.

July 30, 2008

Small molecule entries on the FTP site

Several small molecule structure entries (entry IDs in the 20000 range) have been released and are available from entry files directory on the FTP site. Each entry directory contains NMR-STAR files in both v.3 and v.2.1 formats, coordinate file, constraint file(s), and, if available, AVS report file. We are working on adding these to the entry summary webpage.

March 20, 2008

NMR-STAR V3 Files on FTP site

BMRB has released several of the entries as NMR-STAR version 3 files here:

Version 3 files on FTP

For those in the NMR community wishing to see a preview of what NMR-STAR version 3 files will be like for the purpose of adapting software or reviewing the format, this archive provides a list of clean examples from recent entries.

Recent entries have been annotated entirely in NMR-STAR version 3, and converted back to version 2 for publication on the website. These files provide a view of what the entries contain before being converted back to version 2. In the future, all entries on the BMRB website will be in NMR-STAR version 3 by default (with a link to the NMR-STAR version 2 files so they may be obtained for backward compatibility).

Although NMR-STAR version 3 will become the default way entries are published on the BMRB website, all entries, new and old, will have both a version 2 and a version 3 copy available on the site. This is for backward compatibility with software written for NMR-STAR version 2.

Please try it out and contact us with any comments and suggestions.

April 20, 2007

Chemical Shift Query

BMRB has released a Chemical Shift Query tool. The tool allows you to create tables of chemical shift information by specifying the residue of a protein or nucleic acid. The search query can encompass the entire database, or be limited by BMRB entry, atom name, or range of chemical shifts. The results can be viewed directly on the web page or downloaded as a tab-separated file that can be viewed in a text editor or spreadsheet such as Microsoft Excel.