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On-Q/Legrand DA7559 User Manual

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M. Bach, R. Brunner, J. Stone, K. Vandivort
Version 0.85
June 25, 2002
1
Theoretical Biophysics Group
University of Illinois and Beckman Institute
405 N. Mathews
Urbana, IL 61801
JMV WWW home page:
Description
The JMV User's Guide describes how to run and use the molecular visualization and analysis
program JMV. This guide documents the usage of the graphical user interface for displaying and
grapically manipulating molecules, and describes how to customize the appearance and behavior
of JMV for each user.
1

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  • Page 1 M. Bach, R. Brunner, J. Stone, K. Vandivort Version 0.85 June 25, 2002 Theoretical Biophysics Group University of Illinois and Beckman Institute 405 N. Mathews Urbana, IL 61801 JMV WWW home page: Description The JMV User’s Guide describes how to run and use the molecular visualization and analysis program JMV.

  • Page 2: Table Of Contents

    Contents 1 Introduction 1.1 Credits and Program Reference ......1.2 Copyright and Disclaimer ....... . . 2 Tutorials 2.1 Rapid Introduction to JMV .

  • Page 3: Introduction

    Chapter 1 Introduction JMV is a Java Molecular Viewer written in Java and Java3D. It can be used to load data files to display molecules in common molecular representations and color styles. Users can load files from a URL, from a local file, or from the RCSB databank. Users can also load PDB files when using BioCoRE.

  • Page 4: Credits And Program Reference

    Credits and Program Reference The authors request that any published work or images created using JMV include the following reference: Bach, M., Brunner, R., Stone, J., Vandivort, K. “JMV” JMV has been developed by the Theoretical Biophysics group at the University of Illinois and the Beckman Institute.

  • Page 5: Tutorials

    Chapter 2 Tutorials Rapid Introduction to JMV Here is a quick introduction to JMV. To start, you need Java and Java3D. See the Installation Guide for more details on getting those. From there, you can view JMV in a browser simply by visiting a webpage that uses JMV.

  • Page 6: User Interface Components

    Chapter 3 User Interface Components Once you have JMV started, and have a file loaded, navigation is very simple. The molecule appears in the main canvas and the controls appear below. The mouse controls to orient the molecule are: Left button: Rotate Middle button: Zoom (Moving the mouse down zooms in, moving it up zooms out) Right button: Translate On 2-button mice, the controls are:...

  • Page 7: Loading A Molecule

    Chapter 4 Loading A Molecule The “Load a file” section under the “File” menu brings up the file selection dialog box that allows you to load files to view in JMV. There are 2 types of files JMV can currently read, PDB files and VRML files.

  • Page 8: Molecular Drawing Methods

    Chapter 5 Molecular Drawing Methods Molecular Drawing Methods JMV allows you to view the molecule with different representations. To change the representa- tion, select “Representation” from the “View” menu, and select one of the choices. The current representations available are: 5.1.1 Lines The default representation is ‘Lines’, which is also known as ‘wireframe’.

  • Page 9: Tube

    5.1.6 Tube Tube draws a spline curve that goes through all the “Carbon-alpha” (CA) atoms in the molecule. The spline curve is drawn as a series of cylinders. 5.1.7 Trace Trace draws cylinders connecting the “Carbon-alpha” (CA) atoms in the molecule. This is similar to Tube, except the atoms are directly connected by cylinders, not by a smooth spline.

  • Page 10: Molecule Colors

    Chapter 6 Molecule colors JMV allows you to change the color gradient of the molecule. When selecting a color gradient, JMV uses 3 colors, a beginning, middle, and end color. The gradient fades from the beginning to the middle, and then from the middle to the end color to create a smooth color gradient. The number of “in-between”...

  • Page 11: Saving And Loading Sessions

    Chapter 7 Saving and loading sessions JMV allows you to save a session. Once you get a molecule in a particular representation, color, and orientation that you like, you can then save that session so you can look at it again later, or so that others can view your findings.
  • Page 12 local filesystem. If you selected the “Save a JPEG of the JMV image?” box, then a JPEG file of the molecule window will also be saved to the BioFS and to your local filesystem. You can view saved .jmv files in the same way as PDB files, by selecting the “Properties” link, and the “View this molecule in JMV”...

  • Page 13: Viewing Modes

    Chapter 8 Viewing Modes JMV allows you to view the molecule in stereoscopic view. In stereoscopic view, 2 molecules are drawn, each from a slightly different viewpoint. These views are then switched back and forth very rapidly. When viewed with special glasses, each image is given to one eye, and the image appears in 3d.

  • Page 14: Display Options

    Chapter 9 Display options The “Display Options” choice under the “View” menu brings up a panel allowing you to change display settings in JMV. Lights: The JMV scene has 4 built in lights: A light coming from the front, one from the back, one from the top, and one from the bottom.

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