BMRB News
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October 2, 2009
NMR-STAR files available via REST API
BMRB entries can now be retrieved from the following URLs:
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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/data/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.
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June 10, 2009
Beta NMR-STAR table converter tool
NMR-STAR 3.1 table converter is available for beta testing at
http://pike.bmrb.wisc.edu/software/conv/index2.html.
The tool can convert assigned chemical shifts table to XEASY, TALOS, and Sparky formats. It can
also convert most NMR-STAR 3.1 data tables (not just chemical shifts) to NMR-STAR 2.1.
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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.
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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.
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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.
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July 29, 2008
PDB/BMRB entry matching
With ADIT-NMR, an entry that is being deposited to both BMRB and PDB now comes
through the same tool, from the same site. Several users of BMRB have
stated that it would be useful if there was a direct list of the match
between these entries, for those cases where an entry was being deposited
to both sites. We have made this list
available from the FTP site.
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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.
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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.
Please try it out and contact us with any
comments and suggestions.
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