Macs in Chemistry

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spectroscopy

Mnova 14.0.1 is ready for download.

 

Just got an email

We have fixed bugs and are bringing you some new features in version Mnova 14.0.1 to help you with your analytical data. As usual we would like to thank the people who have contributed by giving us great feedback!.

Download here

Mnova 14.0.1 is a minor release where they have fixed several bugs and also implemented new functionality mainly in NMR, MS and NMRPredict, more details here.


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Mnova 14 is released

 

Mnova 14 has just been released this includes new features in most plugins: NMR, MS, NMRPredict, Screen, DB, Structure Elucidation, and also some new features.

We have added a new module, Mnova ElViS, for Electronic and Vibrational Spectroscopies, as we continue to add new analytical data that can be read, processed, archived and reported using Mnova. For those working on regulated markets and having to comply with 21 CFR Part 11 or GxP rules, Mnova 14 includes brand new Audit Trail and Digital signatures features


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An automated framework for NMR chemical shift calculations of small organic molecules

 

A recent paper in Journal of Cheminformatics describes An automated framework for NMR chemical shift calculations of small organic molecules DOI.

As an alternative, we introduce the in silico Chemical Library Engine (ISiCLE) NMR chemical shift module to accurately and automatically calculate NMR chemical shifts of small organic molecules through use of quantum chemical calculations. ISiCLE performs density functional theory (DFT)-based calculations for predicting chemical properties—specifically NMR chemical shifts in this manuscript—via the open source, high-performance computational chemistry software, NWChem.

Isicle is available from GitHub https://github.com/pnnl/isicle or can be installed using Conda (with required dependencies

conda create -n isicle -c bioconda -c openbabel -c rdkit -c ambermd python=3.6.1 openbabel rdkit ambertools snakemake numpy pandas yaml statsmodels

In addition, ensure the following third-party software is installed and added to your PATH:

cxcalc (license required from ChemAxon, Marvin)
NWChem http://www.nwchem-sw.org/index.php/Download.

ISiCLE is implemented using the Snakemake workflow management system, enabling scalability, portability, provenance, fault tolerance, and automatic job restarting. Snakemake provides a readable Python-based workflow definition language and execution environment that scales, without modification, from single-core workstations to compute clusters through as-available job queuing based on a task dependency graph.

There is more details on Snakemake here.

I've added Isicle to the Spectroscopy Page.


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PythoMS: A Python framework for analysis of mass spectrometric data

 

An interesting publication for those who use Mass Spectroscopy, PythoMS: A Python Framework to Simplify and Assist in the Processing and Interpretation of Mass Spectrometric Data Chemrxiv.

The PythoMS framework introduces a library of classes and a variety of scripts that quickly perform time-consuming tasks: making proprietary output readable; binning intensity vs time data to simulate longer scan times (and hence reduce noise); calculate theoretical isotope patterns and overlay them in histogram form on experimental data (an approach that works even for overlapping signals); render videos that enable zooming into the baseline of intensity vs. time plots (useful to make sense of data collected over a large dynamic range) or that depict the evolution of different species in a time-lapse format; calculate aggregates; and provide a quick first-pass at identifying fragments in MS/MS spectra. PythoMS is a living project that will continue to evolve as additional scripts are developed and deployed.

All available on GitHub under the MIT license https://github.com/larsyunker/PythoMS. This package has been written for python 3.5+.

I've added it to the Spectroscopy page.



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Updated INSENSITIVE

 

Insensitive (Incredible Nuclear Spin EvolutioN Simulation Tool Intended for Visual Education) is an application to simulate the NMR experiment based on the quantum mechanical density matrix formalism.

It is available for Mac OS X 10.6 and above and iOS 5.1.1 and above. Full details can be found in Concepts In Magnetic Resonance, 2011, 38A (2), 17-24 DOI.

The NMR experiment is usually described by a choice of three models that operate on different levels of abstraction: the vector model, the product operator formalism and the density matrix approach. The transition between these models poses a didactic challenge for teacher and student alike. A new computer program is presented, which simulates a spin system on the textbook level and compares the three approaches, with the possibility to manipulate the system at every step. It closes a gap between NMR education and professional simulation tools. Some algorithms are explained, which are used in the simulation to extract information from the density matrix.

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Added MestraNova to Mobile apps

 

I've just added MestReNova to the mobile science site.

MestRe Nova is an iPad app for viewing/manipulation NMR spectra

There are an increasing number of spectroscopy apps available.


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Mnova 12.0.3 (minor release)

 

Update

IUPAC Name

  • Able to name molecules with atoms in non-standard valence
  • Implement skeletal replacement (“a”) nomenclature for heteropolycyclic ring systems
  • Naming of branched ring assemblies
  • Correct names of several suffix groups
  • Able to name ring assemblies of 3-6 identical cyclic systems

MS

  • Precursors m/z values displayed in the MSn extracted spectra title

Full details here http://resources.mestrelab.com/whats-new-mnova-12-0-3/

There is a review of Mnova here


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A Review of MNova NMR

 

MNova NMR is Mestrelab Research’s NMR analysis program that can be used to quickly view, process and analyse both 1D and 2D spectra, as well as to easily produce publication quality assignments and images. The software can be downloaded from Mestrelab’s website (45-day free trial licences are available).

You can read the review here

Picture1

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NMR solvent peaks

 

I just noticed this mentioned on Twitter and so I've added it to the Mobile Science site.

NMR Solvent peaks is a conveniently-searchable version of the ungainly table of NMR data most organic chemists keep a copy of nearby. Instead of searching through the table for a peak near your unidentified peak, just enter your solvent and the peak's multiplicity and location and you'll have a short list of candidate impurities

There is also a web-based version and a twitter feed for submitting bugs and finding out about updates.

There are a number of other NMR apps available


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Collaborative Computational Project No. 4 for Macromolecular X-Ray Crystallography

 

CCP4 exists to produce and support a world-leading, integrated suite of programs that allows researchers to determine macromolecular structures by X-ray crystallography, and other biophysical techniques.

update 047 is out and contains updates to:

Component Description Mac OS 64-bit Linux 32-bit Linux 64-bit Windows 32-bit Windows 64-bit
panddas update to 2.11 yes yes yes - -
Molrep PFMOD correction yes yes yes yes yes
pointless 1.11.6 yes yes yes yes yes
pointless1.11.5 bug fix for multi lattice data yes yes yes yes yes
ccp4i2 fixes in molrep interface yes yes yes yes yes
edstats new version yes yes yes yes yes
ccp4i lorestr: fix for interface yes yes yes yes yes
monomers add 0WD,2Q5,6G6,6ZL,79F,7K9,8LL, 9Q8,FJI,OMZ,QUJ,QVE,RU2,YY9 yes yes yes yes yes
monomers Format fix: CPN,CPO,DEF,GCR,IMF,QPT yes yes yes yes yes
monomers Replace: UAP yes yes yes yes yes
ccp4mg fixes bug which causes MG/MrBUMP to not work for many sequences yes yes yes yes yes
ccp4mg update for https access to PDBe yes yes yes yes yes
mmdb2 False "duplicate sequence number" error in case of short residue names yes yes yes yes yes
numpy update to 1.12.1 yes yes yes - -
scipy update to 1.16.1 yes yes yes - -

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r-maldiquant

 

Just noticed this on Bioconda

r-maldiquant a complete analysis pipeline for matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) and other two-dimensional mass spectrometry data. In addition to commonly used plotting and processing methods it includes distinctive features, namely baseline subtraction methods such as morphological filters (TopHat) or the statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak alignment using warping functions, handling of replicated measurements as well as allowing spectra with different resolutions.

To install

conda install -c bioconda r-maldiquant

More details here http://strimmerlab.org/software/maldiquant/index.html

There are more spectroscopy applications here


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ARIA2 (Ambiguous Restraints for Iterative Assignment)

 

I just came across a publication DOI describing ARIA2 (Ambiguous Restraints for Iterative Assignment) is a software for automated NOE assignment and NMR structure calculation.

ARIA comes as a software library written in the object-oriented programming language Python. The modular design makes it easy for the user to extend and modify the program. The GUI is based on the graphics libraries Tcl/Tk and Tix, interfaced by Python.

ARIA runs on Linux, SGI machines and Mac OS X.

More details can be found on the website http://aria.pasteur.fr.

I've added ARIA2 to the spectroscopy page.


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Mnova updated

 

Mnova 11.0.4 (April 2017) has been released, this is another minor release with some bug fixes such as:

  • Improved NUS processing algorithm: some 2D experiments that showed unexpected noise artefacts are now processed properly by the improved NUS processing algorithm.
  • HSQC stripped transformed in Topspin files loads spectra correctly referenced.
  • All shortcuts (Mac version) are now fully functional.
  • Agilent LCMS files with negative ion traces are now detected appropriately.

Mnova is a multipage, multivendor, multitechnique and multiplatform analytical chemistry software suite designed as a container for various plugins.


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Mnova 11.02

 

The latest version Mnova 11.0.2 is a minor release with improved  automatic phase correction algorithm as main feature as well as some minor bug fixes.

Mnova is a multipage, multivendor, multitechnique and multiplatform analytical chemistry software suite designed as a container for plugins to address different aspects of spectroscopy.

image-mnova

There is also a page dedicated to spectroscopy


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Orange NMR update

 

Orange NMR has been updated.

Orange NMR is an App to predict 13C and 1H NMR spectra: draw a structure to see its spectrum. The accuracy of the algorithm is about 1.9 ppm for 13C and 0.21 ppm for 1H (RMSD=3.4 and 0.31 ppm correspondingly). The number of heavy atoms in structure to predict for free is restricted to 12 atoms. This restriction can be removed by purchasing additional licenses.

  • Instantly re-calculate spectrum while changing structure;
  • Predicted spectra stored in iCloud and synchronised among all iOS devices and Mac version (itunes.apple.com/app/orange-nmr/id680184249);
  • Email PDF report;
  • Zoom in spectrum;
  • Zoom in structure (important for iPhone users);
  • Option to display chemical shift values on structure;
  • Simple clean interface.

The prediction algorithm is derived by: K. A. Blinov, E. D. Smurnyy, T. S. Churanova, M. E. Elyashberg, A. J. Williams, Chemom. Intell. Lab. Syst. 2009, 97, 91

What's New in Version 2.4 More accurate 3J H-H couplings prediction.

There are many more science apps for mobile devices here.

Chemistry on Mobile Devices Meeting


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Mnova 11 released

 

A new update to the popular spectroscopy application Mnova has been announced.

This is a major release that incorporates many new features in NMR, MS, Molecule Editor, Database, Verify and NMRPredict plugins. We have integrated a new PhysChem properties module as well as important enhancements in our Scripting Engine. This version has fixed several bugs.

There is also a page of spectroscopy applications here


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iNMR test release

 

The latest update to iNMR version 6.0.0 is available for testing.

Version 6.0.0 requires Mac OS X El Capitan. Today only 60% of Mac users have it. This doesn’t seem the right moment for replacing version 5. In conclusion, version 6 is currently available for a few selected testers only. Anybody can apply. Testers will receive a key that is going to expire in December. The keys for version 5 are not valid for version 6.

iNMR is a high performance NMR analysis program.

fig_01

See also the spectroscopy page.


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Orange NMR Updated

 

Orange NMR has been updated, with more accurate 4J HH couplings prediction and improvements to the peaks table.

Orange NMR is an App to predict 13C and 1H NMR spectra: draw a structure to see its spectrum. The accuracy of the algorithm is about 1.9 ppm for 13C and 0.21 ppm for 1H (RMSD=3.4 and 0.31 ppm correspondingly).

There are an increasing number of spectroscopy application available for mobile devices.


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Topspin for NMR

 

I've added Topspin to the Spectroscopy page, this is an NMR processing package from Bruker. Looks to be free for academics.

In order to provide students, researchers and teachers with unlimited access to the best tools for off-line NMR processing, Bruker is making their market leading NMR processing software TopSpin available free of charge for all academic users.

There are also an increasing number of spectroscopy application available for mobile devices.


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USPEX Universal Structure Predictor

 

I've added USPEX Universal Structure Predictor: Evolutionary Xtallography to the alphabetical listing of applications

A.R. Oganov, J.C. Schon, M. Jansen, S.M. Woodley, W.W. Tipton, and R.G. Hennig. Appendix: First Blind Test of Inorganic Crystal Structure Prediction Methods, pages 223–231. Wiley-VCH Verlag GmbH & Co. KGaA, 2010.


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Orange NMR Updated

 

Orange NMR the iOS app to predict 13C and 1H NMR spectra has been updated, just draw a structure to see its spectrum.

What's New in Version 2.2

iOS 9 multitasking supported.

Optional calculation of MF, MW, Monoisotopic Mass and Elemental Composition added.

Ability to show terminal and all carbons on structure added.

Some minor bugs fixed.

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ImageVis3D and Orange NMR updates

 

I've just got details of a couple of updates to mobile science apps.

ImageVis3D Mobile is a mobile visualization application one to visualize and share volume and surface data while you are on the go. With ImageVis3D (available for free at www.imagevis3d.com) and ImageVis3D mobile you can transfer your own data directly from the desktop to your mobile device.

What's New in Version 5.1 - new iOS 9 compatible UI (support for Slide Over and Split View) - numerous improvements in the rendering engine - slice viewer visualizes geometry in addition to volume data

imagevis1

Orange NMR is an App to predict 13C and 1H NMR spectra: draw a structure to see its spectrum. The accuracy of the algorithm is about 1.9 ppm for 13C and 0.21 ppm for 1H (RMSD=3.4 and 0.31 ppm correspondingly). The number of heavy atoms in structure to predict for free is restricted to 12 atoms. This restriction can be removed by purchasing additional licenses.

What's New in Version 2.1. Table of peaks added. Structure drawing enhanced: Touch and drag from bond to draw ring. Double click inside ring to make it aromatic. P and I elements added. Help added.

orangenmr

There are now an increasing number of mobile spectroscopy apps available.

Comments

SpeckTackle

 

The latest issue of Journal of Cheminformatics has a paper that might be of interest to a variety of people involved in spectroscopy or data visualsation. SpeckTackle: JavaScript charts for spectroscopy.

We present SpeckTackle, a custom-tailored JavaScript charting library for spectroscopy in life sciences. SpeckTackle is cross-browser compatible and easy to integrate into existing resources, as we demonstrate for the MetaboLights database. Its default chart types cover common visualisation tasks following the de facto ‘look and feel’ standards for spectra visualisation.

SpeckTackle is an open-source JavaScript library to create custom-tailored charts for spectroscopy in life sciences. Implemented charts exist for mass spectrometry, one- and two-dimensional NMR, UV/VIS, IR, and general continuous data use cases such as chromatograms.

The authors kindly supply a demo web page demonstrating different chart types and functions of the SpeckTackle library. Example data is embedded in the web page (800 kb file size). Click on the buttons at the top of the page to see the data displayed. For the Chromatogram, Difference Chart and Spectral Match click the button then the Add Data button.

Highlighting a section of the spectra expands the view and mouseover on the 2D NMR spectra provides a tooltip giving chemical shifts

I've added this to the spectroscopy resources page

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Mobile Science Updates

 

Orange NMR has been updated 1H NMR prediction (12 atoms restriction) added.
Allow to draw structures with S, F, Cl and Br.
13C NMR prediction accuracy improved.

ElementalDB has been updated to version 2.1 to fix a bug to improve display under iOS8. ElementalDB is a really impressive demonstration of the computational abilities of an iPad, allowing chemical structure based searching of the 1.4 million structures within ChEMBL. There is a review of ElementalDB here.

iSpartan a interesting tool for molecular modelling under iOS has been updated.
Now 64-bit enabled.
Improved performance of graphics surface code
iOS 7 improvements for Save, Search by Name, and Sketch palette
Improved notification for job errors when using the Spartan Server feature

Comments

ChemDoodle Web Components JCAMP Interpreter

 

Displaying spectra on the web is usually a pretty minimal experience, often simply an image file. Whilst there a number of desktop applications for viewing spectra, web-based tools were often limited to Java plugins which have now almost completely fallen out of favour.

The JCAMP data format (1) for spectra is pretty widely used and we are starting to see javascript implementations of viewers. This very nice example uses the ChemDoodle web components to display the spectra and provide interaction. Hovering close to a nucleus that has a peak correlation defined will highlight that nucleus and any other nuclei in its group along with highlighting the corresponding peak. Conversely hovering close to a peak that has correlated nuclei associated with it will highlight the set.

(1) JCAMP-DX: A Standard Form for the Exchange of Infrared Spectra in Computer Readable Form ROBERT S. McDONALD and PAUL A. WILKS, JR. Appl. Spectrosc. 42(1), pp151-162, 1988

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Chenomx NMR Suite

 

The latest update to the Chenomx NMR Suite has just been released, this includes a new batch processing wizard and several improvements. I checked with the developers and this update was built on a machine under Mac OS X 10.10 although the website had not yet been updated to include Yosemite compatibility.

There is a listing of spectroscopy applications here, and a comprehensive summary of compatibility of Scientific Applications under Yosemite here.

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Topspin

 

I just added Topspin from Bruker to the list of spectroscopy applications.

Topspin is capable of data processing of 1D and higher dimensional NMR datasets including Fourier transform, window functions, baseline and phase correction, peak picking, integration, line shape analysis (Gauss/Lorentz, dynamic NMR, solids), relaxation and multiplet analysis, spectrum and Fid simulation, printing/plotting, quantification, AU/Python/Macro programming. Optionally NUS processing and small molecule structure elucidation (demo licenses available). For Mac systems the CPU must be capable of executing 64bit-instructions according to “Intel Core 2 Duo” processor type or newer.

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Mnova 9.1.0 released

 

Mestrelab Research have just announced the release of the NMR application Mnova 9.1.0. This release fixes several bugs and incorporates many new features on NMR, MS, the Molecule Editor and the GUI.

This new version also includes the release of the Mnova Screen plugin, an automatic tool for the analysis of ligand screening NMR data.

It also includes a long list of bug fixes


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iNMR has been updated

 

The very popular NMR processing tool iNMR has been updated

The new versions 5.3.7 (for Mac) and 2.3.7 (for Windows), both available since June 20, add Covariance NMR to the processing toolbox. This technique creates a symmetric square matrix, starting from any 2-D matrix. The result can look completely different from the starting spectrum, though the information contained is necessarily the same. An example is hsqc-tocy (a kind of hetero-correlation experiment). After normal processing, it has two different axes: a 1-H axis and a 13-C axes. Starting from here you can apply two different kinds of Covariance. The so-called Direct Covariance creates a symmetric H-H matrix. The so-called Indirect Covariance creates a symmetric C-C matrix. Both are homo-correlation plots.

A more detailed description is available here:

http://nmr-analysis.blogspot.it/2008/10/introduction-to-covariance-nmr.html

This link leads to the pioneer of the method:

https://research.chemistry.ohio-state.edu/bruschweiler/web-servers/370-2/

There are more spectroscopy applications for Mac OSX here

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LSD and CASA added to spectroscopy page

 

I’ve just added to two applications to the spectroscopy page.

LSD (Logic for Structure Determination) is designed to find all possible molecular structures of an organic compound that are compatible with the experimental spectroscopic data.

Structure building relies on connectivity data found in 2D NMR spectra, without any reference to a chemical shift database. Molecular structures containing up to 50 non-hydrogen atoms were investigated by means of the LSD program. The measurement protocol that is required by LSD includes the recording of 1D 1H and 13C as well as 2D COSY, HSQC and HMBC spectra. The status of each atom must be defined. It includes the atom symbol, the hybridization state (sp3, sp2 or sp), the number of attached hydrogen atoms, and the electric charge. This part of the data set is most often easily deduced by the user from elementary chemical shift knowledge. The status of the heteroatoms is deduced from the elemental molecular formula.

The CASA (Computer-Aided Spectral Assignment) program is intended to assign 13C NMR resonances to the carbon atoms in a user-supplied molecular structure.

It relies on an exploitation of chemical shift correlations in 2D NMR spectra and, optionally, on a comparison between experimental and estimated chemical shift values. The assignment of all resonances is possible if the hypothetic supplied structure is the good one, assuming that CASA input data is correct. CASA may therefore be seen as a 1D/2D NMR-based automatic structure verification tool. The result of the CASA program is a set of lists of possible assignments.

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iNMR 5.3.6 released

 

The very popular NMR application iNMR was updated recently to version 5.3.6. This is a minor update:

When the slider for the first-order phase correction reaches the end-of-the-run, a message appears at the center of the same dialog: "Move This!", meaning that, if you want to go further, it's enough to touch the "fine-coarse" selector.

I’ve updated the spectroscopy page to reflect this

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rNMR added to spectroscopy page

 

rNMR is an add-on for R.

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.

I’ve added it to the spectroscopy page.

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Spectroscopy apps for iOS

 

I’ve just been sent details of a number of iOS apps that would be useful to those involved in spectroscopy, (NMR, IR, MS) so I’ve added them all to the mobile science site.

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Learn NMR FID

 

Learn NMR FID is a great teaching tool to learn the basics of NMR data collection and processing. Use simulated free induction decays (FIDs) and spectra to see apodization, noise and relaxation effects. Move peaks and see how the FID changes. Real and imaginary FIDs prior to and after processing are displayed as is the resultant spectrum after the Fourier transform.

There are more science apps for iOS on the mobilescience site.

I also thought I’d mention this framework that was brought to my attention recently. There is a trend to move massively parallel tasks to the GPU, GPU Image is a framework (BSD license) that simplifies the creation of GPU filters. This framework is built around OpenGL ES 2.0, so it will only work on devices that support this API. This means that this framework will not work on the original iPhone, iPhone 3G, and 1st and 2nd generation iPod touches. All other iOS devices are supported.

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ChemDoodle Web Components 6 released

iChemLabs have just announced the release of ChemDoodle Web Components 6, this is a major update to their javascript based chemical structure drawing and rendering package.

One of the most important changes from a developers point of view is the external libs (jQuery, jQuey UI, jQuery plugins, glMatrix) are now included into the ChemDoodle scope. This offers several advantages, including eliminating all library conflicts, reducing the number of files required to be installed, and controls the versions used by ChemDoodle. You can now include these libraries yourself at any version and not worry about conflicts. To use the libraries inside of ChemDoodle, call them from the ChemDoodle.lib closure. When I created the interactive graph using FLOT this was one of the issues.

There is also a new EditorCanvas3D canvas which is the 3D component allowing you to interact with and alter chemical data as the 2D Sketcher does in 2D. The 3D editor supports many new WebGL features including picking, highlighting and measurements (distances, angles and torsions).

Lewis Dot Structure style bonds can now be rendered.

As well as editing and drawing structures ChemDoodle web components provides an means to simulate NMR and mass spectra in a web browser

There are also a number of bug fixes and other improvements.

Please Note

This update includes some major refactors, such as the renaming of the sketcher files and packages and inclusion of the external libraries internal to the ChemDoodle scope, so pay careful attention when upgrading.

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iNMR Offers

I see the developer of iNMR has a number of opportunities to win copies of the excellent iNMR.

Details are here.

As we come up to the start of a new academic year there are also a couple of student promotions.

http://www.inmr.net/fall.html

http://www.inmr.net/annual.html

fig_01

There are more spectroscopy applications here.