This is a listing of the applications available on Mamba, divided by category. We have tried to provide a basic description of the program, how to run it and links to sites on the Internet/Mamba for more information on the program, wherever applicable.
Description: The Insight II molecular modeling program is BIOSYM's 3D graphical environment for molecular modeling. Its powerful interface gives you a seamless flow of data between other BIOSYM programs. Use the Insight II program to create, modify, manipulate, display, and analyze molecular systems and related data. For more information on BIOSYM/MSI and it's products click here.
Run command: This program can be launched by typing insightII
Documentation:Hardcopy documentation is available in BioSciII Rm 5205 for the old version. Hardcopy documentation for the new version (ver. 95) is on order. DO NOT remove the copies marked with "Mamba". Those not so marked can be BORROWED (implies returning) for short periods.
Comments:The latest version of BIOSYM/MSI software has been updated as of 12/31/95. All the standard package and all the Life Science Modules have been installed and should be available. If there is strange behavior, please let me know. We need to order new paper documentation to go with it. As soon as I get them, I'll put them in Mamba's room.
Description:MolScript is a program for creating molecular graphics in the form of PostScript plot files. Possible representations are simple wire models, CPK spheres, ball-and-stick models, text labels and Jane Richardson-type schematic drawings of proteins, based on atomic coordinates in various formats. Colour, greyscale, shading and depth cueing can be applied to the various graphical objects. More information is available from the Molscript homepage.
Run command:This program can be launched by typing molscript.
Documentation:Plaintext documentation is available on Mamba. The Molscript homepage also has documentation available.
Comments:This program requires a X-Windows display.
Description:From the introduction to the Namot2 manual: "Nucleic Acid MOdeling Tool (NAMOT) is a graphic tool to build and manipulate nucleic acid structures. It is built upon the reduced set of coordinates developed here at Los Alamos National Laboratory in collaboration with scientists at the Max-Planck-Institute for Biophysical Chemistry in Goettingen,Germany. Use of these reduced coordinates provide a powerful and intuitive interface to nucleic acid structure. NAMOT2 features a set of user modifiable libraries that provide flexibility for users to expand NAMOT2 to fit their research needs."
Run command:This program can be launched by typing namot2.
Documentation:Documentation is online in HTML format and is available by clicking here.
Comments:This program requires a X-Windows display.
Description: This is Simon Brocklehurst's protein analysis tool, especially useful for visualizing various analyses of protein structure by passing the output through molscript and raster3d. It is a powerful program and produces both useful data and graphics, but it is driven from the command-line, so you'll have to read about it to see how it operates. For more information about this program, click here.
Run command:This program can be launched by typing naomi.
Documentation:Documentation is available online, via the Web. Look here for the Web documentation. Local documentation is available in postscript, text, and HTML (manual and command references) formats.
Comments:This program runs only on Silicon Graphics workstations running Irix 5 or higher (this includes Mamba).
Description:This is Manfred Sippl's Protein Structural Analysis tool (for verifying putative protein structures). Prosa II supports and guides studies aimed at the determination of a protein's native fold. It is helpful for experimental structure determinations and for modeling studies.
Run command:This program can be launched by typing prosaII.
Documentation:Click here for postscript documentation. Web HTML documentation is available here.
Comments: This program runs in X-Windows and ASCII modes. It writes out data as postscript files.
Description:RasMol2 is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images. The program reads in a molecule co-ordinate file and interactively displays the molecule on the screen in a variety of colour schemes and molecule representations. Currently available representations include depth-cued wireframes, 'Dreiding' sticks, spacefilling (CPK) spheres, ball and stick, solid and strand biomolecular ribbons, atom labels and dot surfaces.
Run Command: This program can be launched by typing rasmol.
Documentation:Documentation is available on Mamba in postscript format for the manual and reference card. A Microsoft Word format documentation file is also available on Mamba. The NIH maintains HTML documentation.
Comments: RasMol has been written for Microsoft Windows, Apple Macintosh, UNIX and VMS systems. The UNIX and VMS systems require an 8, 24 or 32 bit colour X Windows display (X11R4 or later). The UNIX version has been installed on Mamba. If you would like to FTP a copy of RasMol for your platform, click here.
Description: From the Raster3D homepage: "Raster3D is a set of tools for generating high quality raster images of proteins or other molecules. The core program renders spheres, triangles, and cylinders with specular highlighting, Phong shading, and shadowing. It uses an efficient software Z-buffer algorithm which is independent of any graphics hardware. Ancillary programs process atomic coordinates from Brookhaven PDB files into rendering descriptions for pictures composed of ribbons, space-filling atoms, bonds, ball+stick, etc. Raster3D can also be used to render pictures composed in Per Kraulis' program MOLSCRIPT in glorious 3D with highlights, shadowing, etc. Output is to pixel image files with 24 bits of color information per pixel."
Run command:This program can be launched by typing render
Documentation:The documentation is in man as well as HTML for raster3d, avs2ps, ribbon, balls, render, rods as well as the Raster3D Home Page, and postscript.
Comments:Programs for previewing and figure composition are written for IRIS4D workstations (GL graphics), but all other code is intended to be machine-independent. There are also some examples of cartoons generated by raster3D in /usr/local/src/raster3d/examples.
Description: From the Interactive Simulations Inc., homepage: "The SCULPT interface and the paradigm embody a radically different approach to computer-based molecular modeling in that it lets a user manipulate a structure in a direct and intuitive manner. SCULPT has made improvements over other modeling systems in that it couples the user's manipulations of a structure to a novel minimization algorithm that is orders-of-magnitude faster than conventional methods. Current features include:
Run command: The demo version of this program is currently on Mamba.
Documentation: Available on Mamba both in postscript and plaintext formats.
Comments: This program requires a GL display and therefore can be run only from Mamba's console. If you wish to try demos of Sculpt, change your working directory to:
/usr/local/src/sculpt
and type
./go
Description:SETOR is a program for displaying macromolecules and is available to non-profit users for a small nominal fee. It allows the display of various kinds of solid models ("ropes", "secondary structure a la Jane Richardson", "stick", "CPK") and a wide range of colouring methods (including changing the background). It can display Connolly surfaces and electron density maps (with varying line widths if you so desire). It has a complete range of captioning and labelling possibilities. It can have multiple light sources (including coloured lights) and one can vary the degree of smoothness of the model and have antialiasing of your final image. Finally it can save output direct to an RGB file (including automatic cropping to the 2/3 ratio of 35mm slide film).
Run command: This program has been installed, but is awaiting a licanse to activate it.
Documentation: A postscript manual is available on Mamba.
Comments: This program requires a GL display, and can therefore be run only from Mamba's console.
Description: This is a comprehensive suite of software for nucleic acid and protein sequence analysis including, but not limited to,
For more information on GCG and its software click here.
Run command:The command line interface of this package can be launched by typing gcg. To launch the X-Windows version of this program, type wpi at a UNIX shell prompt.
Documention: Hard copy documentation is available in Bio Sci II Room 5205. To get help for the command line interface type genhelpafter having entered the program (by typing gcg). Web HTML documentation for the command line interface is also available here. Web documentation for the X-Windows version is available here.
Comments:This package can be run remotely using either the command line interface via a telnet session or the X-Windows interface if your local computer can start a X-session.
Description: Written by Joseph Felsenstein, this is a free package of 31 programs for inferring phylogenies, including programs to carry out parsimony, compatibility, distance matrix, invariants ("evolutionary parsimony") and likelihood methods on a variety of different kinds of data. For more about PHYLIP, go to the PHYLIP home page.
Run command: The program(s) can be launched by typing the individual program name (see the documentation section) at a UNIX shell prompt.
Documentation: Plaintext documentation is available on Mamba. Web HTML documentation is also available here.
Comments:MS-DOS, MS Windows, Macintosh and Power Macintosh executables are also available for PHYLIP. If you are interested in installing PHYLIP for your platform, click here.
Description:From the AVS home page: "AVS includes a comprehensive suite of data visualization and analysis capabilities that make it the most complete Visual Computing Environment available. AVS incorporates both traditional visualization tools such as 2D plots and graphs and image processing as well as advanced tools such as 3D interactive rendering and volume visualization. You don't have to be an application developer to take advantage of the sophisticated capabilities of AVS. If you need a point-and-click visual application to view your data, AVS provides intuitive, easy-to-learn interfaces to the most frequently used visualization techniques. These interfaces, or "viewers", can help you explore your data immediately -- even before you begin to tailor AVS for your specific needs." For a more detailed look at AVS and its other products, click here.
Run command:This program can be launched by typing avs.
Documentation:Although hardcopy documentation is not yet available, there is extensive online documentation available.
Comments: This program requires a X-Windows display.
Description: As the name indicates, another wizardly tool for image analysis. It primarily consists of the ImageMagick image display tool, which first determines the hardware capabilities of your workstation. If the number of unique colors in an image is less than or equal to the number the workstation can support, the image is displayed in an X window. Otherwise, the number of colors in the image is first reduced to match the color resolution of the workstation before it is displayed.
In addition to the image display program, ImageMagick also has command line programs that perform these functions:
Run Command: This program can be launched by typing the name of the appropriate ImageMagick tool. For more information on the ImageMagick tools, click here.
Documentation:Documentation for each ImageMagick tool is available in manand can be viewed by typing man [name of tool].
Comments:This program requires a X-Window display. A HTML FAQ file for the tools is maintained here.
Description:The SDSC image tools are tools developed at the San Diego Supercomputer Center (SDSC) to handle image manipulation and file format conversion for a wide range of file formats. For more information about this program and its capabilities, click here.
Run command: This program can be launched by typing imconv.
Documentation: Available on Mamba, type imconv -fullhelpto read the man pages.
Comments:For a look at the graphics formats supported by this program, click here.
Description:Written by John Bradley, XV is an interactive image manipulation program for X Windows that converts image files to and from GIF, JPEG, TIFF, PBM, PPM, X11, bitmap, Sun rasterfile, RLE, RGB, BMP, PCX, and PM formats.
Run command:This program can be launched by typing xv.
Documentation:Postscript documentation is available on Mamba.
Comments:This program requires a X-Window display.
We have tried to be as accurate as possible in describing these programs. However, if you find any mistakes, better links or have any comments in general, please mail me.