NMR View: A computer program for the visualization and analysis of NMR data

Summary NMR View is a computer program designed for the visualization and analysis of NMR data. It allows the user to interact with a practically unlimited number of 2D, 3D and 4D NMR data files. Any number of spectral windows can be displayed on the screen in any size and location. Automatic peak picking and facilitated peak analysis features are included to aid in the assignment of complex NMR spectra. NMR View provides structure analysis features and data transfer to and from structure generation programs, allowing for a tight coupling between spectral analysis and structure generation. Visual correlation between structures and spectra can be done with the Molecular Data Viewer, a molecular graphics program with bidirectional communication to NMR View. The user interface can be customized and a command language is provided to allow for the automation of various tasks.Inquiries concerning the availability of NMR View and the Molecular Data Viewer should be sent via email to johnsonb@merck.com or to Bruce A. Johnson, Merck Research Laboratories, RY80Y-103, P.O. Box 2000, Rahway, NJ 07065, U.S.A.     

Madeline 2.0 PDE: a new program for local and web-based pedigree drawing

The Madeline 2.0 Pedigree Drawing Engine (PDE) is a pedigree drawing program for use in linkage and family-based association studies. The program is designed to handle large and complex pedigrees with an emphasis on readability and aesthetics. For complex pedigrees, we use a hybrid algorithm in which consanguinous loops are drawn as cyclic graphs whenever possible, but we resort to acyclic graphs when matings can no longer be connected without line crossings. A similar hybrid approach is used to avoid line crossings for matings between distant descendants of different founding groups. Written in object-oriented C++ and released under the GNU General Public License (GPL), Madeline 2.0 PDE reads input files specified on the command line and generates pedigree drawings without user interaction. Pedigree output in scalable vector graphics (SVG) format can be viewed in browsers with native SVG rendering support or in vector graphics editors. We provide an easy-to-use public web service, which is experimental and still under development. Availability: http://kellogg.umich.edu/madeline.     

GCI: A network server for interactive 3D graphics

The Graphics Command Interpreter (GCI) is an independent server module that can be interfaced to any program that needs interactive three-dimensional (3D) graphics capabilities. The principal advantage of GCI is its simplicity. Only a limited set of powerful features have been implemented, including object management, global and local transformations, rotation, translation, clipping, scaling, viewport operations, window management, menu handling and picking.GCI and the master (client) program it serves run concurrently, communicating over a local or remote TCP/IP network. GCI sets up socket communication and provides a 3D graphics window and a terminal emulator for the master program. Communication between the two programs is via ASCII strings over standard I/O channels. The implied language for messages is very simple. GCI interprets messages from the master program and implements them as changes of graphical objects or as text messages to the user. GCI provides the user with facilities to manipulate the view of the displayed 3D objects interactively, independently of the master program, and to communicate mouse-controlled selection of menu items or 3D points as well as keyboard strings to the master program.The program is written in C and initially implemented using the Silicon Graphics GL graphics library. As the need to link special libraries to the master program is completely avoided, GCI can very easily be interfaced to existing programs written in any language and running on any operating system capable of TCP/IP communication. The program is freely available.     

ESPript: analysis of multiple sequence alignments in PostScript.

MOTIVATION: The program ESPript (Easy Sequencing in PostScript) allows the rapid visualization, via PostScript output, of sequences aligned with popular programs such as CLUSTAL-W or GCG PILEUP. It can read secondary structure files (such as that created by the program DSSP) to produce a synthesis of both sequence and structural information. RESULTS: ESPript can be run via a command file or a friendly html-based user interface. The program calculates an homology score by columns of residues and can sort this calculation by groups of sequences. It offers a palette of markers to highlight important regions in the alignment. ESPript can also paste information on residue conservation into coordinate files, for subsequent visualization with a graphics program. AVAILABILITY: ESPript can be accessed on its Web site at http://www.ipbs.fr/ESPript. Sources and helpfiles can be downloaded via anonymous ftp from ftp.ipbs.fr. A tar file is held in the directory pub/ESPript.     

An interactive graphics program for comparing and aligning nucleic acid and amino acid sequences.

This paper describes a computer program designed to look for similarities between pairs of nucleic or amino acid sequences. The program looks both for segments of perfect identity or for regions where, using a scoring matrix, a minimum value is exceeded. The results of comparisons are presented as a matrix which is displayed on a simple graphics terminal. Use of a graphics terminal allows the user to display the whole of the two sequences in one screenful or to home-in on regions of interest to examine them in more detail. The program is interactive and so the user can easily see the effect of changes to variables and can use inbuilt editing functions to make insertions to produce alignments of the two sequences. These aligned sequences can then be saved on disk files for further processing.     

VisiCoor: A simple program for visualization of proteins

A well-drawn picture acts as an excellent metaphor for something real, and human vision provides instant, random access to any part of which the picture represents. It is in this sense that pictures can convey information more effectively than words alone. The power of the graphics work-stations available today makes visual presentation of scientific results a reality. A molecular graphics program for investigating protein structures, as well as several sample plots that show the power of the program, are presented.     

Molecular conformational space analysis using computer graphics: Going beyond FRODO

The molecular graphics program FRODO has been modified to support analytical animation of molecular dynamics trajectories. The enhanced program, mdFRODO, supports all features available in FRODO and is interfaced to GROMOS. A variety of analytical animation modes is included. Extensive coloring and atom selection features are implemented to aid the user in distinguishing features of interest in a set of conformations. Molecular conformational space can be analyzed efficiently and comprehended. Animations may be viewed in stereo, and the animated object can be overlaid with any of the standard FRODO objects. The mdFRODO program is of wide use in molecular dynamics, X-ray crystallography and two-dimensional NMR work. Examples illustrating various aspects of collective motion in protein molecules are given and discussed.     

SED88: a Pascal program for the analysis of sedimentation equilibrium data

Analytical ultracentrifugation is commonly used for the determinationof molecular weights (sedimentation equilibrium) and sedimentationcoefficients (sedimentation rate) of biological macromoleculesin solution. A Turbo Pascal program for the analysis of sedimentationequilibrium centrifugation data produced by absorbance opticalsystems is described. The user may enter data from a scan ofabsorbance versus distance from the centre of rotation, viaa graphics tablet (or ASCII file). This is subsequently manipulatedto yield an apparent weight average molecular weight for thegiven sample. Plots of In (absorbance) versus (radius²) mayalso be produced. The method described uses readily availablecomputational equipment requiring only a graphics tablet inaddition to an IBM PC compatible computer. This technique andthe software developed have been used to investigate the molecularweight range of two International Humic Substances Society (IHSS)reference samples from the Suwannee River. Received on October 7, 1988; accepted on December 12, 1988     

MeV+R: using MeV as a graphical user interface for Bioconductor applications in microarray analysis

We present MeV+R, an integration of the JAVA MultiExperiment Viewer program with Bioconductor packages. This integration of MultiExperiment Viewer and R is easily extensible to other R packages and provides users with point and click access to traditionally command line driven tools written in R. We demonstrate the ability to use MultiExperiment Viewer as a graphical user interface for Bioconductor applications in microarray data analysis by incorporating three Bioconductor packages, RAMA, BRIDGE and iterativeBMA.     

MOLPACK: molecular graphics,for studying the packing of protein molecules in the crystallographic unit cell

A graphics program, MOLPACK, has been developed on the Silicon Graphics IRIS-4D computer system for displaying the packing of proteins in the crystallographic unit cell. In addition to the normal viewing operations of rotation, translation and scaling, the program has the ability to translate molecules along the cell axes while maintaining their crystallographic equivalent positions within the unit cell. This allows the user to observe the packing of protein molecules generated by molecular replacement, to create a new packing model or to locate an unknown molecule. A special feature of the program is that up to four independent molecules can be manipulated in the asymmetric unit.     

XmMol: An X11 and motif program for macromolecular visualization and modeling

XmMol is a desktop tool designed to provide both interactive molecular graphics on X11 displays and easy interface with external applications. A kernel provides an interactive wire-frame display of macromolecules. It supports depth cueing, 3D clipping, and stereo. Various representations, coloring, and labeling modes are proposed. Docking and interactive back-bone deformation tools are also supported. Communication protocols allow the user to develop new external features or to use XmMol as a visualization tool for external numerical programs.     

Diving in uncharted waters: An updated genetics toolkit highlights the challenges of polyploidy in landscape genomics analyses

As molecular ecologists, we have by necessity become adept at working across computational platforms. A diverse community of scientists has developed a broad array of analytical resources spanning command line to graphical user interface across Linux, Mac, and Windows environments and a dizzying array of program‐specific input formats. In light of this, we often explore our data like free divers – filling our lungs with air and descending for a short period of time into one part of our data set before resurfacing, reformatting, and preparing for our next analysis. In this issue of Molecular Ecology Resources, Meirmans (2020) presents an updated version of GenoDive, a program with a toolkit that provides users with the opportunity to stay a while and delve deeper into the diverse portfolio of information provided by a genomic data set. The comprehensive nature of GenoDive coupled with its unique capability to handle both diploid and polyploid data also provides an opportunity to reflect on the unevenness of resources available for the analysis of polyploid versus diploid data. Since new updates include the addition of plug‐ins for genotype‐environment association analyses, we limit the observations presented here to the common tools used for landscape genomics analyses.     

HAMOG: Molecular graphics program for chemistry 5 biochemistry 5 molecular biology and enzyme research

HAMOG is a computer graphics program written in C for personal computers. Clear menus and a contextsensitive help option make the program easy to operate for occasional users. HAMOG provides a flexible environment for displaying and manipulating molecules and molecular systems. Special functions allow the investigation of structure-activity relationships of biologically active molecules. These include the calculation of molecular electrostatic potentials and fields, the superposition of molecules and the calculation of steric accessibilities. The visualization and manipulation of protein structures immediately readable from the Brookhaven Protein Data Bank files are also possible using HAMOG. The construction of any peptide or protein structure is very simple.     

Z-curve: a computer program calculating DNA helical axis coordinates for three-dimensional graphic presentation of curvature.

In order to predict curvature of DNA fragments, we previously developed a computer program for simply calculating a vectorial sum of all individual roll, tilt and twist wedge angles between the nearest base pairs for a given DNA fragment [Lee et al., (1991)]. Now, a new program, called Z-curve, was developed to calculate three-dimensional coordinates of the helical center of each base pair along the DNA, using helical axis deviations from B-form DNA by wedge angles. The output file of the new program was designed to become an input file for a graphics program, Insight II. Thus, we were able to obtain three-dimensional graphic presentations of DNA helical axis curvatures of any length. It visualized spatial details of the DNA curvature, where and how much it curves, and to which direction. It also allowed calculation of the three-dimensional distance between two ends of a DNA fragment, which could provide a measure of its curvature. Here, three DNA fragments, both curved and straight, were subjected to the Z-curve and Insight II programs. The results showed that their curvature details could be visualized to the level of the base pair, whether the DNA fragments contained an oligo(A) track or not. Their estimated curvatures were consistent with the experimental results of permutation gel mobility assay.     

A graphical interface for the FoldX forcefield

SUMMARY: A graphical user interface for the FoldX protein design program has been developed as a plugin for the YASARA molecular graphics suite. The most prominent FoldX commands such as free energy difference upon mutagenesis and interaction energy calculations can now be run entirely via a windowed menu system and the results are immediately shown on screen. AVAILABILITY AND IMPLEMENTATION: The plugin is written in Python and is freely available for download at http://foldxyasara.switchlab.org/ and supported on Linux, MacOSX and MS Windows.     

msap: a tool for the statistical analysis of methylation‐sensitive amplified polymorphism data

In this study msap, an R package which analyses methylation‐sensitive amplified polymorphism (MSAP or MS‐AFLP) data is presented. The program provides a deep analysis of epigenetic variation starting from a binary data matrix indicating the banding pattern between the isoesquizomeric endonucleases HpaII and MspI, with differential sensitivity to cytosine methylation. After comparing the restriction fragments, the program determines if each fragment is susceptible to methylation (representative of epigenetic variation) or if there is no evidence of methylation (representative of genetic variation). The package provides, in a user‐friendly command line interface, a pipeline of different analyses of the variation (genetic and epigenetic) among user‐defined groups of samples, as well as the classification of the methylation occurrences in those groups. Statistical testing provides support to the analyses. A comprehensive report of the analyses and several useful plots could help researchers to assess the epigenetic and genetic variation in their MSAP experiments. msap is downloadable from CRAN ( http://cran.r-project.org/ ) and its own webpage ( http://msap.r-forge.R-project.org/ ). The package is intended to be easy to use even for those people unfamiliar with the R command line environment. Advanced users may take advantage of the available source code to adapt msap to more complex analyses.     

PEPCRE: an interactive program to create,manipulate and display oligopeptides

PEPCRE is an interactive computer graphics program for the rapid construction, manipulation and display of oligopeptides. Essentially any desired conformation of an oligopeptide can be constructed in a simple and straightforward manner. The program provides various display and output possibilities. It is user-friendly and is written in FORTRAN 77 for use on inexpensive, monochrome graphics terminals.     

Tek FRODO: A new version of FRODO for Tektronix graphics stations

A new version of the molecular graphics program FRODO was developed to allow the range of Tektronix graphics stations to be used for molecular modeling and crystallographic applications. The work was divided into two parts: first, the universal molecular modeling graphic package (Tek_MMGP) was written to enable basic modeling operations for Tektronix stations. Second, all routines of FRODO involving computer graphics were modified to fit the new hardware environment, and linked with Tek_MMGP. The resulting package, Tek_FRODO, has been used successfully for crystallographic refinement in several projects. The program, written in FORTRAN, is ready to be ported to any of Tektronix 3D graphics stations; it is available from the authors on request.