RNMR.NMRFAM.WISC.EDU

rNMR: Open Source Software for NMR Data Analysis

Open Source Software for NMR Data Analysis. RNMR is an open source software package for visualizing and interpreting one and two dimensional NMR data. In contrast to most existing 2D NMR software, rNMR is specifically designed for high-throughput assignment and quantification of small molecules. As a result, rNMR supports extensive batch manipulation of plotting parameters and has numerous tools for expediting repetitive resonance assignment and quantification tasks. The most powerful features of rNMR ar...

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rNMR: Open Source Software for NMR Data Analysis | rnmr.nmrfam.wisc.edu Reviews

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Open Source Software for NMR Data Analysis. RNMR is an open source software package for visualizing and interpreting one and two dimensional NMR data. In contrast to most existing 2D NMR software, rNMR is specifically designed for high-throughput assignment and quantification of small molecules. As a result, rNMR supports extensive batch manipulation of plotting parameters and has numerous tools for expediting repetitive resonance assignment and quantification tasks. The most powerful features of rNMR ar...

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rNMR: Open Source Software for NMR Data Analysis | rnmr.nmrfam.wisc.edu Reviews

https://rnmr.nmrfam.wisc.edu

Open Source Software for NMR Data Analysis. RNMR is an open source software package for visualizing and interpreting one and two dimensional NMR data. In contrast to most existing 2D NMR software, rNMR is specifically designed for high-throughput assignment and quantification of small molecules. As a result, rNMR supports extensive batch manipulation of plotting parameters and has numerous tools for expediting repetitive resonance assignment and quantification tasks. The most powerful features of rNMR ar...

INTERNAL PAGES

rnmr.nmrfam.wisc.edu

1

rNMR: Data

http://rnmr.nmrfam.wisc.edu/pages/data/data.html

We have compiled a subset of data from the BMRB. Biological Magnetic Resonance Data Bank) and converted it to UCSF format for use in rNMR. The libraries posted to the right contain spectra of 270 common metabolites collected under standardized conditions. An example dataset taken from a red blood cell metabolism study is also provided along with a brief tutorial (below) showing how rNMR's ROI feature can be used to document NMR resonance assignments. November 17, 2009.

2

rNMR: Release Notes

http://rnmr.nmrfam.wisc.edu/pages/download/release_notes.html

Version 1.1.9 (February 9, 2015). The ROI table and peak list editing GUIs,. Have been modified to update their respective tables and refresh the spectrum automatically. In addition, view buttons have been added to enable zooming to the selected ROI/peak, along with a Refresh (manually refresh spectrum) and a Restore button (restores ROI/peak lists to their state prior to their respective GUI being opened). The auto ROI function,. Internal peak picking function,. Modified calls to function. Simplified an...

3

rNMR: Help

http://rnmr.nmrfam.wisc.edu/pages/help/help.html

For step-by-step instructions on using rNMR, take a look at the rNMR user manual. Or the instructional videos found below (also available on YouTube. For documentation on a specific rNMR function use the help topics link. A link to the R help pages and search engine has also been included as an added convenience. Converting Bruker and NMRPipe spectra. Graphics and plot settings. 1D slices and projections. Regions of interest (ROIs). Last updated: June 12, 2013.

4

rNMR: Downloads and Installation

http://rnmr.nmrfam.wisc.edu/pages/download/download.html

RNMR is an add-on package developed for R, a free statistical computing envirionment. Versions of rNMR are available for Windows, Mac, Linux and Unix using the links on the right. The rNMR package requires R version 2.10 or higher. R can be downloaded free of charge from www.r-project.org. Install R (2.10 or higher). Download rNMR for Windows. Run the rNMR installation program. Install R (2.10 or higher). Download rNMR for Linux. Run the rNMR installation program. Ubuntu 8.04 (Hardy Heron) and up. RNMR r...

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macinchem.org

Spectroscopy | Macs in Chemistry

http://www.macinchem.org/spectroscopy.php

MacOS X Spectroscopy Applications. Spectroscopy Applications for MacOSX. Since many people appear to be searching the site for spectroscopy applications I thought I'd compile a list. Remember that many of the more expensive applications have free/cheap education or student versions. Updated 5 May 2016. Click on the table headers to sort. Http:/ www.inmr.net/. Several licensing options, specifically written for MacOSX, with spotlight and quicklook plugins. Now linked to DOSY toolbox. 0, paid support.

pine.nmrfam.wisc.edu

NMRFAM Software Downloads

http://pine.nmrfam.wisc.edu/download_packages

We acquire minimal information for statistics (only used in grant applications and reviews). Please fill the boxes below downloading (required)! Link to [NMRFAM Pulse Program Downloads]. Link to [NMRFAM Script Downloads]. Link to [NMRFAM Official Web Site]. Link to [NMRFAM Software Descriptions]. Please use FireFox or Google Chrome for downloading. In other way, you can just ask for a link. Varian (Agilent) - Linux. NMRFAM-SPARKY / Enhanced PyMOL / NMRmix. Ponderosa Client / Ponderosa Analyzer.

pacsy.nmrfam.wisc.edu

PACSY main page

http://pacsy.nmrfam.wisc.edu/index.html

Example of Pacsy Maker. Example of Pacsy Analyzer. CSV-formatted version of PACSY is now downloadable from here (Monthly Updated). MolProbity Analysis is now added as MOLPROB DB table! PACSY reference correction and statistics from Dr. Keith Fritzsching. PACSY RAMA is downloadable. Check our download page. Try PACSY web service below:. Tip Use PACSY Analyzer program to create SQL query easy. J Biomol NMR. 2012 Oct;54(2):169-79. Lee W, Yu W, Kim S, Chang I, Lee W, Markley JL. Last Updated: July 16, 2015.

pine.nmrfam.wisc.edu

NMRFAM Software Downloads

http://pine.nmrfam.wisc.edu/download_packages.html

We acquire minimal information for statistics (only used in grant applications and reviews). Please fill the boxes below downloading (required)! Link to [NMRFAM Pulse Program Downloads]. Link to [NMRFAM Script Downloads]. Link to [NMRFAM Official Web Site]. Link to [NMRFAM Software Descriptions]. Please use FireFox or Google Chrome for downloading. In other way, you can just ask for a link. Varian (Agilent) - Linux. NMRFAM-SPARKY / Enhanced PyMOL / NMRmix. Ponderosa Client / Ponderosa Analyzer.

nmrml.org

nmrML - home

http://nmrml.org/tools

The nmrML development team has also fostered and coordinated the creation of nmrML aware webservices and tools covering a large fraction of a typical NMR data acquisition and processing workflow, i.e. to generate, convert, process, validate and publish nmrML files. Additionally, we have worked closely with open source and commercial tool developers to encourage nmrML format adoption. A summary table of available nmrML compatible tools is available below. Converts vendor to nmrML format. Interactive NMR S...

areca.nmrfam.wisc.edu

ARECA@NMRFAM

http://areca.nmrfam.wisc.edu/help.html

NOESY contacts analyses ▼. NMRFAM Servers ▼. For any question or concern please contact Hesam Dashti (dashti@nmrfam.wisc.edu). Chemical Shift Assignments options. BMRB NMRSTAR v2.1:. In the NMRSTAR v2.1 files the chemical shift assignments should start with a header that explains the data contents. In the following example the necessary tags that ARECA looks for are tagged in an example of NMRSAR v2.1 file:. Atom shift assign ID. Residue author seq code. Chem shift value error. Chem shift ambiguity code.

areca.nmrfam.wisc.edu

ARECA@NMRFAM

http://areca.nmrfam.wisc.edu/ncp/ncp_analysis

NOESY contacts analyses ▼. NMRFAM Servers ▼. Statistics on the expected number of short-range NOESY contacts. Provides probabilities of NOESY contacts. In ARECA. ALA (Avg. 13.277). CYS (Avg. 13.492). ASP (Avg. 13.522). GLU (Avg. 13.869). PHE (Avg. 14.506). GLY (Avg. 11.805). HIS (Avg. 14.347). ILE (Avg. 14.460). LYS (Avg. 14.702). LEU (Avg. 14.676). MET (Avg. 14.304). ASN (Avg. 13.902). PRO (Avg. 13.745). GLN (Avg. 14.155). ARG (Avg. 14.783). SER (Avg. 13.357). THR (Avg. 13.902). VAL (Avg. 14.268).

areca.nmrfam.wisc.edu

ARECA-NOESY Contacts Probabilities@NMRFAM

http://areca.nmrfam.wisc.edu/ncp/nrg_analysis

NOESY contacts analyses ▼. NMRFAM Servers ▼. Statistical Analysis on Protein NOESY Distance Restraints. Caluclating statistics on the number of reported NOESY distance restraints per residue for proteins. We downloaded the parsed simple NOESY distance database from the NRG ( http:/ restraintsgrid.bmrb.wisc.edu/. The entries containing nucleic acids were removed. 5836 entries (proteins) were used for our statistical analysis. The histogram of the ratio is shown in Fig. 1.

areca.nmrfam.wisc.edu

ARECA-NOESY Contacts Probabilities@NMRFAM

http://areca.nmrfam.wisc.edu/ncp

NOESY contacts analyses ▼. NMRFAM Servers ▼. In NMR studies of proteins it is useful to have the probability of NOESY contacts between two protons. We have developed a module for validating chemical shifts assignments against NOESY data ( ARECA. And as a part of this module we calculated the probabilities of short-range NOESY contacts in two ways:. We used structures deposited at the PACSY. Database and filter them by the use of the MolProbility. In addition we used the TINKER molecular modeling. A stati...

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rNMR: Open Source Software for NMR Data Analysis

Open Source Software for NMR Data Analysis. RNMR is an open source software package for visualizing and interpreting one and two dimensional NMR data. In contrast to most existing 2D NMR software, rNMR is specifically designed for high-throughput assignment and quantification of small molecules. As a result, rNMR supports extensive batch manipulation of plotting parameters and has numerous tools for expediting repetitive resonance assignment and quantification tasks. The most powerful features of rNMR ar...

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