On-Q/Legrand DA7559 User Manual Download

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JMV User’s Guide

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:

http://www.ks.uiuc.edu/Development/jmv/

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.

http://www.ks.uiuc.edu/

Summary of Contents for DA7559

Page 1: ...MV WWW home page http www ks uiuc edu Development jmv 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 http www ks uiuc edu ...

Page 2: ...ts 6 4 Loading A Molecule 7 5 Molecular Drawing Methods 8 5 1 Molecular Drawing Methods 8 5 1 1 Lines 8 5 1 2 Bonds 8 5 1 3 CPK 8 5 1 4 VDW 8 5 1 5 Licorice 8 5 1 6 Tube 9 5 1 7 Trace 9 5 2 Coloring Methods 9 6 Molecule colors 10 7 Saving and loading sessions 11 7 1 Saving a session 11 7 2 Loading a saved session 11 7 3 Loading and saving in BioCoRE 11 8 Viewing Modes 13 9 Display options 14 2 ...

Page 3: ...http www ks uiuc edu Development jmv List of key JMV features General molecular visualization JMV has the ability to read PDB files and view the molecules in common representations and color schemes Applications JMV can be run as an applet as a standalone application or within another application VRML files JMV can also read in VRML version 2 0 files This makes it possible to view molecular repres...

Page 4: ...ty of Illinois and the Beckman Institute The main authors of JMV are M Bach R Brunner J Stone K Vandivort This work is supported by grants from the National Institutes of Health grant number PHS 5 P41 RR05969 04 the National Science Foundation grant number BIR 9423827 EQ and the Roy J Carver Charitable Trust 1 2 Copyright and Disclaimer JMV is Copyright c 2000 2002 Theoretical Biophysics Group and...

Page 5: ... 85 jar may use a different number in place of 0 85 depending on the version 2 2 Viewing a molecule Titin Once you have JMV started you can load a molecule in a number of ways Select Load a file from the File menu This will bring up a dialog box asking for a file name Type in 1TIT and click Load This will load the molecule Titin from the RCSB a repository of molecular files The screen should displ...

Page 6: ...nvas 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 Left button Rotate Left button ALT Zoom Moving the mouse down zooms in moving it up zooms out Right button Translate 6 ...

Page 7: ...u wish to view into the text field and press the Load button The file should be displayed The Protein Data Bank is a repository for many pdb files Each file stored there is identified by a unique 4 digit code If you know that code you can load the molecule in JMV Type in the 4 digit code in the text field in the dialog box that appears Click the Load button and the molecule will be displayed In ad...

Page 8: ...second atom 5 1 2 Bonds Nearly everything about this option is the same as lines except that instead of drawing a bond as a line between two atoms a cylinder is drawn instead 5 1 3 CPK CPK is a combination of Bonds and VDW in that it draws the atoms as spheres and also draws the bonds connecting them The sphere are drawn much smaller than in VDW and the cylinders are thinner than in Bonds Each sph...

Page 9: ...tifier In the Index color scheme JMV creates a color gradient that creates a smooth color transition going through each atom in order of their index numbers Resname In the pdb file each atom belongs to a certain residue The Resname color scheme assigns a color to each Residue Name based on the gradient and colors each residue with the given color Chain In the pdb file each atom belongs to a certai...

Page 10: ...the number of items being colored For example if the molecule is colored by index then each atom gets its own color If the molecule is colored by residue each residue type will get its own color The representations Name and Structure have their own color schemes and are not affected by the color gradients To change the color gradient select Color Gradient from the View menu and select one of the c...

Page 11: ...mage button is checked a JPEG file will be saved with the same name as the jmv file but with the extension jpg This is a picture of the JMV molecule window 7 2 Loading a saved session To load a saved session select Load session from the File menu From the pop up window either type in the path to a jmv file on your system or select one from your local system with the Browse button Load the JMV file...

Page 12: ...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 link in the pop up window that is displayed 12 ...

Page 13: ...an turn it on by selecting the Stereo checkbox under the View menu For Solaris 1 At a command prompt type afbconfig proc Look for the line saying Current resolution setting and write it down You may want this information if you change your stereo settings 2 Type afbconfig res stereo This command puts your X server into stereo mode 3 Log out of your current session and relog in The resolution may b...

Page 14: ...s may be selected If all lights are off the scene will appear blank Sphere resolution You can change the resolution of the spheres in JMV making spheres appear smoother or rougher Decreasing the resolution of the spheres will make the scene move faster in rotation but will make the molecule look less sharp Increasing the resolution of the spheres will make the spheres appear smoother but can make ...

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