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| Quick Links |
NMR data processing
| Molecular graphics and molecular modeling | Structure determination and analysis | Other useful
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AutoAssign |
Bragi |
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| NMR data processing and analysis |
AutoAssign is a constraint-based expert system for automating the analysis of backbone resonance assignments using NMR spectra of small proteins. The program has been trialed on only a few systems here at UConn Health Center with limited success. |
Felix can be used for both NMR data processing and NMR data analysis. However, specialized analysis programs such as XEASY, SPARKY, and NMRView are better suited for analyzing multidimensional NMR data for the purpose of resonance assignment and structure determination. However, several Felix features, such as lineshape analysis of overlapping peaks, can be useful. The powerful macro language of Felix can also be used to create customized tools. We have also found Felix to be useful in the analysis of NMR relaxation data. Please remember that our license only allows two people to run Felix simultaneously, so please be kind and close the program when you are not using it. |
Modelfree is a program for the analysis of 15N or 13C NMR relaxation data using the Lipari-Szabo "model free" approach. 15N or 13C relaxation rates, along with 1H-15N or 1H-13C NOEs, are used as input. |
A program for processing NMR data. NMRPipe is based on UNIX pipes, which allow programs running simultaneously to exchange streams of data under user control. In an NMRPipe processing scheme, a stream of spectral data flows through a pipeline of processing programs, each of which performs one component of the overall scheme, such as Fourier transformation or linear prediction. Complete multidimensional processing schemes are constructed as simple UNIX shell scripts. A major advantage of NMRPipe is the ability to distribute processing tasks on multi-CPU computers and computer networks allowing for very fast processing compared to Felix. NMRPipe has no built-in graphical user interface but instead uses the program nmrDraw for visualization of processed data. Unlike Felix, NMRPipe is free and we have no restrictions on the number of users. NMRPipe is run by executing a simple shell script that you create with all of the processing parameters. See the in-house NMRPipe Script Generator for help in creating processing scripts. |
NMRView is a program for visualization and analysis of NMR datasets. It appears to be very powerful but so far it has not been used extensively by users of the facility. It has the advantage of being scriptable using Tcl/Tk. The NMR groups at Scripps provide a site with additional NMRView documentation and downloadable scripts. |
SPSCAN is a program for semi-automatic assignment of NMR spectra of biological macromolecules. SPSCAN was developed to interface with XEASY, however it also reads spectra in NMRPipe and Bruker (2rr, 3rrr) formats. All output is compatible with DYANA. SPSCAN can be used to integrate NOESY spectra, pick peaks in 3D spectra if you know their positions in two dimensions, extract coupling constants from ECOSY type spectra, convert spectra between various formats, and much more. |
TALOS is a database system for empirical prediction of phi and psi backbone torsion angles using a combination of five kinds (HA, CA, CB, CO, N) of chemical shift assignments for a given protein sequence. The TALOS approach is an extension of the well-known observation that many kinds of secondary chemical shifts (i.e., differences between chemical shifts and their corresponding random coil values) are highly correlated with protein secondary structure. TALOS uses the secondary shift and sequence information to make quantitative predictions of phi and psi angles, and to provide a measure of the uncertainties in these predictions. |
Tensor is a program for the analysis of NMR relaxation data using the extended Lipari-Szabo type analysis. The program can analyze proteins with either an isotropic, axially symmetric, or fully asymmetrical rotation. In addition the program has a graphical display of internal mobility parameters and a rigorous Monte Carlo analysis of errors and model suitability. |
VINCE (VIsualization of Nuclear ConnEctivity) is a computer program for generating graphs summarizing nuclear Overhauser effects (NOEs) observed in proteins, in a form that is commonly used for publication. In addition, Vince can display secondary structure assignments, calculate and display chemical shift indices, or display other user-supplied data. Data are accepted in a variety of file formats, and the program permits interactive data entry. Some simple error-checking is performed on NOE data input files, and a brief sequence summary is provided. Output is in postscript format. |
XEASY is a program for analyzing both 2D and 3D NMR data sets of biological molecules. While initial file set-up can be tricky, it is a very powerful tool for making sequential assignments and extracting distance restraints. Some of its nicest features include the ability to easily make strip plots and its seamless integration into DYANA and MOLMOL. |
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| Molecular graphics and molecular modeling |
Bragi is a molecular modeling program that was originally designed for homology modeling of proteins with unknown structure and the design of proteins with new properties. However, the program has many other features. See the Bragi manual for more details. |
InsightII is a comprehensive molecular visualization and modeling program produced by Accelrys. It only runs on SGI computers. |
MOLMOL is a program for displaying, analyzing, and manipulating molecules. MOLMOL is free and runs on most computer platforms. While MOLMOL may be a little tricky to learn to use it is very powerful for analyzing protein and nucleic acid structures and can be used to produce very high quality images suitable for publication. Output from MOLMOL can also be rendered with the program POV-Ray to produce even higher quality images. |
MolScript is a program for creating schematic or detailed molecular graphics images from molecular 3D coordinates, usually, but not exclusively, protein structures. The user supplies an input file (the script) which specifies the coordinate file, what objects to render and the exact appearance of the objects through the graphics state parameters. There is a helper program MolAuto, which produces a good first-approximation input file from a coordinate file. |
POV-Ray creates three-dimensional, photo-realistic images using a rendering technique called ray tracing. It reads in a text file containing the object and lighting and genterates an image of that object from the point of view of a camera also described in the text file. POV-Ray is slow, but produces high quality images with realistic reflections, shading, and other effects. We generally use it with the program MOLMOL for producing high quality images of biomolecules. Sometimes POV-Ray may cast shadows that detract from the image. In these cases use the shadowless command as described on page 69 of the POV-Ray manual. On the linux machines there is a program called povfront which is a nice GUI to the POV-Ray program. |
RasMol is a molecular graphics program intended for the visualization of proteins, nucleic acids and small molecules. The program is aimed at display and teaching. While simple to use, it significantly less powerful and less capable of generating high-quality images than MOLMOL, InsightII, and VMD. New users should consider using the more powerful Protein Explorer 2, a RasMol derivative. |
The Raster3D molecular graphics package consists of a core program renderer and a number of ancillary programs which read atomic coordinates from Brookhaven PDB files to produce scene descriptions for input to renderer. Raster3D can also render images composed using other programs such as MolScript and XtalView. |
VMD is a program designed for interactive visualization and analysis of biopolymers such as proteins, nucleic acids, and lipids. Many people use VMD for monitoring molecular dynamics simulations and for producing high quality output images. Output images can be further improved by rendering with the program Raster3D. |
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| Structure determination and analysis |
Amber is the collective name for a suite of programs that allow users to carry out molecular dynamic simulations, particularly on biomolecules. |
CNS (Crystallography & NMR System) is a program for the determination of three dimensional structures either from X-ray crystallographic or NMR data. The program has been designed to provide a flexible multi-level hierachical approach for the most commonly used algorithms in macromolecular structure determination. Highlights include heavy atom searching, experimental phasing (including MAD and MIR), density modification, crystallographic refinement with maximum likelihood targets, and NMR structure calculation using NOEs, J-coupling, chemical shifts, and residual dipolar coupling data. |
DYANA is a software package for determination of three dimensional protein and nucleic acid structures on the basis of conformational restraints derived from NMR experiments. DYANA uses torsion angle dynamics which has proven to be robust and efficient for structure calculations. DYANA also interfaces well with XEASY for iterative rounds of structure calculation. Also included with DYANA is the program NOAH which attempts to perform automated assignments of 15N and 13C edited NOESY spectra, HABAS for making stereospecific assignments, and COFIMA for manipulating Cartesian coordinates and distance and dihedral-angle restraints. The latest version (renamed CYANA) has an improved automated assignment program (CANDID) that has already been used with much success at UConn Health Center. |
PROCHECK is a program for analyzing the quality of experimentally-determined protein structures. PROCHECK-NMR is a program that specifically checks structures determined using NMR data. The program checks for covalent geometry, planarity, dihedral angles, chirality, non-bonded interactions, main-chain hydrogen bonds, disufide bonds, stereochemical parameters. |
PROMOTIF provides details of the location and types of structural motifs in proteins of known structure by analysis of PDB coordinate files. |
WHAT IF is a versatile protein structure analysis program that can be used for mutant prediction, structure verification, molecular graphics, etc. |
X-PLOR is a program for the determination of three dimensional structures of molecules based on X-ray crystallographic or NMR data. We often use X-PLOR to refine initial structures determined using CYANA or DYANA. Note that CNS is the latest version of X-PLOR. |
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| Other useful programs |
AGADIR is a program for prediciting the helical content of proteins from the amino acid sequence based on helix/coil transition theory. AGADIR considers only short range interactions. Conditions such as pH, temperature, and ionic strength are considered in the calculations. Manual | AGADIR Home Page |
ALSCRIPT produces beautiful sequence alignment figures in PostScript format. The input files are a multiple sequence alignment in AMPS, CLUSTAL, or GCG format and a file containing the formatting commands. ALSCRIPT is not a multiple sequence alignment program, nor is it an alignment editor. |
Grace is a WYSIWYG tool to make two-dimensional plots of scientific data. Its capabilities are roughly similar to GUI-based programs like Sigmaplot or Microcal Origin plus script-based tools like Gnuplot or Genplot. Its strength lies in the fact that it combines the convenience of a graphical user interface with the power of a scripting language which enables it to do sophisticated calculations or perform automated tasks. |
MOLEMAN2 is a program for the manipulation of pdb files. It is intended for structural biologists who need to do all sorts of formatting of pdb files when converting between various programs. |
XV is an interactive image manipulation program. It can operate on images in GIF, JPEG, TIFF, PBM, PGM, PPM, XPM, X11 bitmap, Sun Rasterfile, Targa, RLE, RGB, BMP, PCX, FITS, or PM format. |
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| NMR file converters |
f2xe converts processed felix.mat files to XEASY format. Referencing information from Felix is retained during the conversion. Usage: f2xe filename(without extension). Example: f2xe polx_hnha (Enter). |
gradsort_p2p | gradsort_p2p rearranges raw Varian data that has been collected with sensitivity enhancement to a format suitable for States or States-TPPI processing in any NMR data processing program. This step is needed when processing sensitivity-enhanced data with Felix, but is not needed with NMRPipe if the Rance-Kay switch is used in data conversion. Usage: gradsort_p2p input output ni ni2 ni3 np. Generally the fid file is renamed from fid to fid.var before running gradsort_p2p. Example: mv fid fid.var; gradsort_p2p fid.var fid 128 32 0 1024. Note that the new filename will be called fid, suitable for conversion to Felix or NMRPipe format. Also, for 3D data sets ni3=0 and for 2D data sets ni2=0 and ni3=0. |
interleave.prl | interleave.prl is an in-house perl script that extracts multiple 2D data sets that were collected in an interleaved mode. This script will separate out the individual files, perform a gradsort on each data set, and convert each one into Felix format to be processed. The usage is interleave.prl output_prefix #_experiments ni np array_flg. The array_flg should be 1 if array = "relaxT, phase" and 0 if array = "phase, relaxT". This can be determined by looking in the procpar file. Note that this program must be run from within the filename.fid directory. |
pipe2flx | pipe2flx converts processed NMR data in NMRPipe format to Felix format. Usage: pipe2flx -in filename -out matrix_name. Example: pipe2flx -in polx_hnha.ft3 -out polx_hnha.mat. |
v2f_grad | v2f_grad combines the gradsort_p2p conversion and the var2flx conversion in a single step. You must be located outside of the Varian subdirectory to run this script. Usage: v2f_grad filename(without extension) ni ni2 ni3 np. Example: v2f_grad polx_hnha 128 32 0 1024. The original Varian data is renamed to fid.var and is saved, while the intermediate file called fid is deleted. A new file with a *.dat extension is created suitable for processing in Felix. |
var2flx | var2flx converts raw varian NMR data to Felix format suitable for processing. Usage: var2flx (Enter). Type in the name of the varian *.fid directory and a new name with a .dat extension when prompted. The byte-swap mode should be set to 0. |
varian | varian runs a graphical program that allows conversion of raw Varian NMR data to nmrPipe format suitable for processing. This program attempts to read in the procpar file and extract parameters; however, be careful, as it is often wrong. It also does not use the correct spectrometer frequency when referencing. The in-house NMRPipe Script Generator may also be used to create scripts for converting Varian data to NMRPipe format. |
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