BNL Structural Biology

Beamline H9B Software Guide

This guide provides a brief overview of all the software available for H9B users. Detailed help in using the new tools can be obtained by contacting Gail Schuman on ext 7985. For help with SANALYSIS, the contacts are either Dieter Schneider on ext. 3423, or Vito Graziano on ext. 4738.

1. SANALYSIS - SANALYSIS is the old, text-based data analysis package for use at H9B. It can provide transmission and cross section calculations, data array integrations, data manipulations, color maps and plots of integrated data. The program also generates a history or journal of all actions taken.

2. ANALYSIS - A new analysis tool designed to provide data reduction and analysis capabilities in a graphics-based program is now available. This software was developed using Motif so it requires X-terminal capabilities. The software is available on both BNLH9B (at the HFBR) and BNLSTB (Building 421). The main menu options are shown in figure 1, and are selected using the mouse. Documentation available from Gail, and help screens have been built into the program at appropriate places. Additional help is available from Gail, (x7985). The ANALYSIS manual is available on the web, but only in postscript form. To access the program from the either the guest2 or guest1 account, just type analysis at the prompt and it will start...providing you are using an X-terminal or workstation.

3. PV-Wave - PV-Wave is a commercial data analysis and graphics tool currently available at BNL through the Central Scientific Computing Facility (CSCF). It resides on the main VAX cluster and can be accessed by anyone on site using a variety of platforms. There are a limited number of licenses ("seats") available, so occasionally access may be restricted. If users find that this is an attractive package, we will consider purchasing our own license for unlimited users on a single machine, such as the VAX in the Structural Biology building (BNLBIO). This tool can provide color maps of the data arrays from H9B, with image processing routines and a variety of color tables for looking at the details of the data. A script has been developed which will provide a quick look at the data with histogram equalization, using any of the 16 available color tables, and will generate a color postscript output file which can be printed on the color printer in building 421. A sample of the color output is in figure 2. This program can run on either a Silicon Graphics or a VAX. The output to the screen can be for an X-terminal or for a VT340, (and a lot of others as well). Gail has the documentation and can help with learning how to use this tool.

4. SAOimage - SAOimage is a package for image analysis developed at the Smithsonian Astrophysical Observatory and is available on both VAXes (BNLH9B at the HFBR and BNLSTB in building 421) and the Silicon Graphics (currently only on BNLVGX in building 421). It can display to any X-terminal. This provides a quick look at data images and has some nice interactive color table adjustments for looking at detailed structure in the image. There are also some limited image processing options available. There is high quality gray scale postscript output available, but color output must be generated using a UNIX tool called SNAPSHOT on the SGI, Print Screen on a VAX X-terminal display, or XV (described here also), on either machine. These color options are not super, but they are an improvement over the LJ-250 color maps. The best choice is to use the VAX version because then no file reformatting has to be done as there is when using the Silicon Graphics. To use SAOimage on the VAX, you must log onto one of the VAXes, (guest1/2 accounts exist on both). The files must be resident on the machine you are logged onto due to a problem that SAOimage has in parsing the node names. Before running, execute a setup file by entering SAOSETUP at the DCL prompt. Once the setup file is executed, to run SAOimage, just enter SAOIMAGE at the prompt. The user can use the command line parameters or enter the parameters inside of the program once it has started. See the documentation or type SAOHELP at the prompt for online help. Gail has the documentation on SAOimage and can help you learn how to use this also. A sample gray scale output is included in figure 3.

5. XV - XV is a program developed at the University of Pennsylvania by John Bradley, (thank you, John). It has capabilities for displaying and saving a large number of file formats, (e.g., TIFF, GIF, JPEG, etc.). It can also store output in postscript form, (both color or B&W), but cannot read Postscript input (yet). It can grab a picture off the screen and allow you to manipulate the color table and then save it in postscript for printing later. The output form allows you to place the picture on the page. Help is available online by typing HELP XV at the prompt. Documentation is also available from Gail. Either Vito or Gail can provide additional assistance. To access this program, just enter XV at the prompt.

6. RASMOL - Molecular Visualization software. This requires that you use an X-terminal or workstation for the graphical display of molecules in several input formats, including PDB format. Gail has copies of the manual if you would like to use this software. We are currently running version 2.5 of RasMol. The PC version (RasWin for windows) is also available if that is preferred.

7. Others - There are a wide variety of display tools and printing tools available at BNL within the Biology department. Please ask about anything you would normally use and maybe we have it here as well. If we don't have it now, it may be something we can add in the future, or it may be available through the main computing facility. Talk to Gail if you have any questions about software availability. There are also lots of program development tools and Internet browsers available...just ask and we can help you find things.