Free nmr software for linux

nmr-relax is designed for the study of the dynamics of proteins or other macromolecules though the analysis of NMR relaxation data. It is a community driven project created by NMR spectroscopists for NMR spectroscopists.
It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of the NOE, reduced spectral density mapping, and the Lipari and Szabo model-free analysis.
Main features:
Supported NMR theories
- The following relaxation data analysis techniques are currently supported by relax:
- Model-free analysis (Lipari and Szabo, 1982a; Lipari and Szabo, 1982b; Clore et al., 1990)
- Reduced spectral density mapping (Farrow et al., 1995, Lefevre et al., 1996)
- Exponential curve fitting (to find the R1 and R2 relaxation rates)
- Steady-state NOE calculation
Data analysis tools
The following tools are implemented as modular components to be used by any data analysis technique:
- Numerous high-precision optimisation algorithms
- Model selection (dAuvergne and Gooley, 2003)
- Akaikes Information Criteria (AIC)
- Small sample size corrected AIC (AICc)
- Bayesian or Schwarz Information Criteria (BIC)
- Bootstrap model selection
- Single-item-out cross-validation (CV)
- Hypothesis testing ANOVA model selection (only the model-free specific technique of Mandel et al., 1995 is supported)
- Monte Carlo simulations (error analysis for all data analysis techniques)
- Model elimination - the removal of failed models prior to model selection (dAuvergne and Gooley, 2006)

nmr-relax is designed for the study of the dynamics of proteins or other macromolecules though the analysis of NMR relaxation data. Its primary purpose is for the Lipari and Szabo model-free analysis of the R1 and R2 relaxation rates together with the steady state heteronuclear NOE. The program also supports relaxation curve fitting for the calculation of the R1 and R2 rates and their errors, the calculation of the NOE and its error, and reduced spectral density mapping.

Flexibility

The aim of relax is to provide a seamless and extremely flexible environment able to accept input in any format produced by other NMR software, able to faultlessly create input files, control, and read output from various programs including Modelfree and Dasha, output results in many formats, and visualise the data by controlling programs such as Grace, OpenDX, and MOLMOL.

All data analysis tools from optimisation to model selection to Monte Carlo simulations are inbuilt into relax. Therefore the use of additional programs is optional.

The power of Python

The flexibility of relax arises from the choice of either relaxs scripting capabilities or its Python prompt interface. Extremely complex scripts can be created from simple building blocks to fully automate data analysis. A number of sample scripts have been provided to help understand script construction. In addition, any of Pythons powerful features or functions can be incorporated as the script is executed as an arbitrary Python source file within relaxs environment.

XDrawChem is a two-dimensional molecule drawing program for Unix operating systems. XDrawChem is similar in functionality to other molecule drawing programs such as ChemDraw (TM, CambridgeSoft).
It can read and write MDL Molfiles, and read ChemDraw text and binary files, to allow sharing between XDrawChem and other chemistry applications, and it can create images in popular formats like PNG and EPS. XDrawChem has been tested on Linux, SGI IRIX 6.5, Sun Solaris, Mac OS X, and Windows.
Main features:
- 100% compatible Windows 95/98/NT version
- Fixed length, fixed angle drawing.
- Automatic alignment of figures. Detects structures, text, and arrows and places them automatically.
- Can automatically draw rings and other structures - has all standard amino acids and nucleic acids in built-in library.
- Can retrieve structures from a network database based on CAS number, formula, or name.
- Can draw symbols such as partial charge, radicals, etc.
- Can read MDL Molfiles, CML [Chemical Markup Language, defined in J. Chem. Inf. Comput. Sci.39(1999), 928-942], ChemDraw(TM) binary format, ChemDraw(TM) XML text format.
- Can write MDL Molfiles, CML, ChemDraw(TM) XML text format.
- Can also read and write any format supported by the current release of OpenBabel.
- Can export pictures in PNG, Windows bitmap (*.bmp), Encapsulated PostScript (EPS), and Scalable Vector Graphics (SVG).
- Can generate 3-D structures with the help of the external program BUILD3D.
- Online help, including tool tips.
- 13C-NMR prediction, based on Bremser W, Mag. Res. Chem.23(4):271-275
- 1H-NMR prediction, based on additive rules and functional group lookup methods, described in Pretsch, Clerc, Seibl, Simon, "Tables of Spectral Data for Structure Determination of Organic Compounds", 2ed., 1989, Springer-Verlag
- Simple IR prediction.
- Simple pKa estimation.
- Octanol-water partition coefficient estimation.
- Reaction analysis: gas-phase enthalpy change estimate, 1H NMR and 13C NMR comparison.
- Integration with OpenBabel, allowing XDrawChem to read and write over 20 different chemical file formats.

Chemsuite is a set of programs designed for the processing of chemical information on Linux/X11. It is free software and released under GPL.
It requires the QT GUI library version 2.3.1 from Trolltech Inc. . It intends to run primary on Linux, but we think it can compile and run on othe Unices.
Chemsuite is composed by several program:
- Chem2D: A 2D molecular drawer.
- Molcalc: A molecular weight calculator
- ChemModel3D: Molecular 3D modeler
- ChemIR: An infrared spectra processor. It can read, process, export and print Perkin Elmer spectra.
- ChemNMR: 1D NMR Processor
- ChemMC: Monte carlo Simulator and Integrator
Enhancements:
- chem2d new engine
- chemIR print spectra bug corrected
- Supports GNU configure utility

Gabedit is a Graphical User Interface to Gaussian, Molcas, Molpro and MPQC computational chemistry packages.
Gabedit includes graphical facilities for generating keywords and options, molecule specifications and ther input sections for even the most advanced calculation types Gabedit includes an advanced Molecule Builder.
You can use it to rapidly sketch in molecules and examine them in three dimensions. You can build molecules by atom, ring, group, amino acid and nucleoside. You can also read geometry from a file. Most major molecular file formats are supported.
Gabedit includes a Gaussian, Molcas, Molpro and MPQC Calculation Setup window which allows you to set up Gaussian, Molcas, Molpro and MPQC jobs in a simple and straightforward manner.
Gabedit includes a text editor for editing Molcas, Molpro, Gaussian and MPQC input files.
Gabedit can graphically display a variety of Gaussian, Molcas, Molpro, MPQC and (partially) ADF calculation results, including the following:
- Molecular orbitals.
- Surfaces from the electron density, electrostatic potential, NMR shielding density, and other properties.
- Surfaces may be displayed in solid, translucent and wire mesh modes.
- Surfaces can be colored by a separate property.
- Contours (colorcoded).
- Planes (colorcoded).
- Dipole
- XYZ axes and the principal axes of the molecule.
- Animation of the normal modes corresponding to vibrational frequencies.
- Animation of the rotation of geometry, surface, dipole, xyz and the principal axes of the molecule.
- Animation of contours.
- Animation of colorcoded planes.
Gabedit can display IR and Raman computed spectra. Gabedit can generate a povray file for geometry (atoms + bonds, including hydrogens bond), surfaces (including colorcoded surfaces), contours, colorcoded planes.
Gabedit can save picture in PPM, BMP , (JPEG) and PS format. Gabedit can generate automatically a series of pictures for animation (vibration, geometry convergence, rotation, contours, colorcoded planes).