Accept-NMR uses an input PDB file, generate symmetry-related copies of a biological molecule of interest, and predict specific user-defined classes of intermolecular contacts between these (using a user-defined distance cutoff). Sort and analyze the resulting contacts, and visualize the results using several visualization schemes in PyMOL. Predict NMR spectra, and specifically the positions of intermolecular contact cross-peaks, based on the contacts predicted and chemical shift table. It is written in Perl, utilizing Gtk2-Perl bindings to provide a cross-platform compatible graphical user interface,
Added to the Spectroscopy page.
Mnova 8.1.1 is a minor release that fixes several bugs in Mnova NMR, MS and the installation process.
Capability to update gamma value of a DOSY spectrum depending on the detected nucleus
- Withewashed view looked wrong in 2D spectra
- Peaks integrated using Peaks method did not get deleted
- Problem copy/pasting a spectrum from Mnova to MS Word as OLE
- Wrong order on assignments reported by Assignments script
- Problems opening a document with deleted molecules and with the compounds table linked to the Page Navigator
There is a page of spectroscopy applications for the Mac here.
I noticed this in the iNMR newsletter.
FREE FOR EVERYBODY Only today 22nd Feb, anybody can ask for a free key for iNMR reader 5. No questions asked. iNMR reader 5 is a 64-bit application that requires Snow Leopard (or a later OS).
A new iNMR reader is available after many months. Instead of restarting from the old version, I have started from the full edition(which includes CPM, DOSY, relaxation times and many other things missing in the old reader), from which I have removed just three commands: Save, Export and Console. In practice it's the iNMR you have appreciated in the past year at a much lower price. Another thing that changes is the key: the old key isn't good. If you already have a license, please wait until March to install this new version and ask for the key. There is no upgrade fee to pay, but remember that a disposable license can't be moved to another computer. You will receive the key valid for your old computer. To ask for a new key, please send the old one back.
The Collaborative Computing Project for NMR was updated last night. No details are available.
The Collaborative Computing Project for NMR (CCPN) is a project that aims to bring together computational aspects of the scientific community involved in NMR spectroscopy of biological molecules, especially those who work in the field of protein NMR. The CcpNmr software suite is a series of programs for macromolecular NMR spectroscopy integrated with the CCP data model. Between programs written by the CCPN, external contributions, and ‘outside’ programs integrated with the data model, it is the intention to provide one suite of programs to carry out all tasks needed in macromolecular NMR spectroscopy. The nature of the data model guarantees that any other program or suite that interfaces with the data model can be used alongside or instead of the CcpNmr suite.
CCPN will be giving a demonstration at the EUROMAR conference during the first week of July (see http://www.euromar.org/). They will also be handing out CDs with the latest release.
There is a page of spectroscopy applications for Mac OS X here.
The latest Mac version of iNMR is 5.2.4, released today. Due to popular demand it restores the slider for zero-order phase correction, which reappears side-by-side with the knob that has been in its place for a whole year. Their function is equivalent. This seems to be a case where it's better to have redundant controls.
I was wondering when someone would use an iPad as the front-end to a fully featured modelling package running on a remote server, looks like Wavefunction have done a pretty impressive job with taking their sophisticated Spartan computational chemistry package from the desktop to mobile devices.
iSpartan creates molecules as familiar 2D sketches, directly converts these into 3D structures, and calculates low energy conformations. Atomic and molecular properties, NMR and infrared spectra, molecular orbitals and electrostatic potential maps are available from a 5,000 molecule subset of the Spartan Spectra and Properties Database (SSPD). The database may also be searched by substructure. Properties, spectra and graphical models of molecules in the SSPD subset are available for examination.
iSpartan Server is an available add-on to the iSpartan app. iSpartan Server installs on a Windows or Macintosh computer and converts iSpartan from an application whose primary utility is sketching molecules in 2D and visualizing them in 3D, into an open-ended molecular modeling research tool providing access to the full Spartan Spectra and Properties Database (SSPD), currently ~170,000 molecules) and to the computational engines used to produce the data in the SSPD. For molecules not included in the database, connection to iSpartan Server supports calculation of structures, properties, and spectra for all user generated molecules from iSpartan running on the iPad, iPhone, and iPodTouch.
There is a listing of science apps for iOS here
Maltcms, short for "Modular Application Toolkit for Chromatography Mass-Spectrometry" is an application framework mainly suited for developers working in the domain of bioinformatics for metabolomics and proteomics. Its aim is to provide reusable, efficient datastructures, abstracting from the various low-level data-formats like netcdf (ANDIMS), mzXML, mzData and mzML and providing consistent access to data features like mass spectra, chromatograms and metadata. Furthermore, Maltcms provides a platform for the implementation and execution of processing pipelines. New and existing algorithms can be easily implemented or included and executed together with existing processing elements
Maui - Maltcms User Interface is also in beta testing.
Maui is an application for visualization, exploration and processing of raw data from GC/LC-MS and GCxGC-MS experiments. Release 1.0 beta2 Available Features
- chromatogram view (1D and 2D) with interactive selection of mass spectra and database query
- integration of custom scripts for raw data and csv type data via Groovy
- charting of csv and raw data
- import and visualization of Maltcms processing results
- interactive peak exploration
- manual refinement of peak lists
- statistical evaluation of peak tables
- 3D viewer with interactive peak exploration for 2D chromatograms based on jzy3D
- GNU-R integration
- 3D PCA viewer
- pipeline runner for Maltcms
I’ve added OpenChrom to the Spectroscopy Page. OpenChrom is an open source software for chromatography and mass spectrometry based on the Eclipse Rich Client Platform (RCP). Its focus is to handle mass spectrometry systems (e.g. GC/MS, LC/MS, Py-GC/MS, HPLC-MS) data files natively. OpenChrom is able to import binary and textual chromatographic data files, such as *.D chromatograms from Agilent Technologies or NetCDF.
Just got this message I thought I’d pass on.
The iNMR reader will remain at €39 for another 5 days only. Staring from Tuesday, it will return to its old (historical) price of € 50. The same applies for the student promo and the laptop extensions, everything that now costs €39 will cost €50 starting from next Tuesday.
iNMR is the only NMR software expressly written for Mac OS X, it uses Mac technologies and is tightly integrated with Mac OS X.
There is a listing of spectroscopy applications here.
After many months of beta testing the latest version of the popular Mac dedicated NMR spectroscopy application iNMR5 has been released. The key new features are tabulated below.
- Version 5 requires a 64-bit Intel chip and Snow Leopard. Version 4 is 32-bit Universal Binary and requires Tiger.
- real-time dragging
- When you drag the margins of the plot, or the integrals, or most of the objects, the plot is continuously updated. Overlay manager
- The Overlay Manager becomes non-modal and can be enlarged to show the full path of the individual documents. Sorting the overlays is simpler and more transparent.
- Manual phase correction
- The zero-order correction is controlled by a knob that never reaches the end of the run. The fine-coarse selector has many more stops. The phase panel is more compact.
- Other dialogs
- “Units and Scales” and “Colors and Levels” change the corresponding plots as soon as you click into a control. The Preferences dialog includes a “Preview” button. The color panel is no more modal. When the open dialog is open, the corresponding menu item isn't dimmed anymore. The console is more compact than in the past, but can be enlarged at will.
- Fit to overlay
- Fitting a simulated spin system is visibly faster.
- The new cursors are more specific. The horizontal palette has a single row of buttons.
- Info tool
- The interpolator is faster, more predictable and more reliable.
- The visual effect of the command ”New Page” is realistic.
- The printed area is no more centered and no more clipped.
- Shows an estimate of the T1.
Depending on your existing license you may be eligible for a free upgrade, for other users there is a small upgrade fee.
There is a list of spectroscopy applications for the Mac here