Introduction

MDV was developed as a molecular graphics server to be used and implemented in a variety of applications. As currently implemented, MDV will display an unlimited number of molecules, in a variety of forms, including:

stick

cylinders

ball & stick

cpk

MDV is a GL graphics system. Versions are available for Silicon Graphics and IBM RS-6000 workstations. An OpenGL version will be available soon. The AIX version requires appropriate graphics cards, however.

This document is not meant to be a programmers manual for implementing a client-server MDV application. Rather, it contains a full description of the commands which may be sent to MDV for execution or entered by using the popup menus available within the application.

Commands and capabilities specific for NMRView may be found elsewhere. Press here for those commands.

User Interface

The interface for MDV is controlled by using the mouse. The client may also send commands for execution. These commands are described below. The command mimic the mouse based interface in an almost one-to-one manner.

The mouse buttons (left,middle,right) are currently mapped as follows:

left
Controls the translation of the global view in the screen oriented x and y axes.

middle
Controls the interactive rotation of the global view. The rotation simulates a virtual trackball.

left-middle
Controls the interactive scaling of the global view. Moving to the right causes a positive scaling of the view. Moving to the left will cause a negative scaling of the view.

Atoms may be picked by using the left mouse button and simultaneously holding down the ALT key on the keyboard. If an atom is selected, the atom name will appear next to the atom. The label may be obscured if the display type is set to anything other than stick.

When the right mouse button is pressed inside the display area, a control popup menu is displayed. A description of the popup menu items follows:

User Interface
A toggle button to turn on and off the entire MDV mouse interface.

Spin Mode
Normally, the middle mouse button may be used to cause the global view to enter a spinnign motion. Hold down the middle mouse button and move in the direction of desired spin. Release the mouse after a short distance and the view will spin. The faster the mouse movement, the faster the spining motion. This button toggles the spin effect.

Reset Transformations
Reset the global viwing matrix to identity.

Display Projection
A pullright option menu to select the desired projection type for the global view, either parallel or perspective. The default when entering MDV is parallel.

Display Type
A pullright option menu to select the desired display type for all molecules, either stick, cylinders, ball & stick or cpk. The default display type for all new molecules is stick.

Atom Labels
A pullright option menu to change the form of atom label display. Atom labels may consist of any combination of atom name, residue name, residue number and molecule name. The default atom label consists of the atom name only.

Anti-Aliasing
A toggle button to turn on and off anti-aliasing of polylines. The default is to antialias all lines.

Depthcueing
A toggle button to turn on and off depthcuing of polylines. The default is to not perform depthcueing.

Save RGB File
Create an SGI RGB image file of the current display. Not available under _AIX.

Command Summary

The following commands are currently available:

color
change colors of molecules or background
radius
set radius for spheres in ball&stick and cpk display modes
create
create new molecules
delete
delete molecules
default
set default molecule for selections
display
change display mode for specific molecules
exit
exit from the server
labels
toggle global display of atom labels
parallel
display mode to parallel projection
perspective
display mode to perspective projection
reset
reset global viewing matrix to identity
scale
scale the current view by a given amount
toggle
toggle various options including display type, antialiasing, etc.
view
center view about specific molecule
visible
toggle visibility of specific molecule
psdump
create postscript file of current display
savewindow
create SGI rgb image file of current display

Command Descriptions

color background reg green blue
color molecule[s] color_name
color molecule[s] red green blue
The color command is used to change various color attributes within MDV. All molecule names must be entered using the PSL syntax. All RGB values must be entered as integer values between 0 and 255. Valid color names are:
yellow
red
green
blue
cyan
magenta
white
byatom

radius keyword value
Set the radius of the given spheres or cylinders types. Radius values must be input as floating point numbers. Valid keywords are:
cylinder
ball
tube

exit
quit
Terminate the MDV server. All connections to the server are closed and the server is shut down.

parallel
Set the global viewing mode to parallel projection. This is the default when MDV is started.

perspective
Set the global viewing mode the perspective projection.

create
Create a new molecule within the MDV server. Users will not normally use this command since molecule creation is usually handled automatically within the client program.

reset
Reset the global viewing matrix within MDV to identity.

psdump
Create a postscript file of the current MDV display. The file is called mdv.ps.

savewindow
Available on the SGI version of MDV. Creates an RGB file of the current display. The file is called scene.rgb.

toggle keyword
Toggle several types of display parameters within MDV. Valid keywords are:

delete molecule_name[s]
Delete the specified molecules from the MDV server. All molecule names must be entered in PSL form.

default molecule_name
Change the default molecule for selection. See PSL documentation. The global view is also centered about this molecule. Only one molecule is required. If more than one molecule is given, the first is the parsed list is used.

display molecule_name[s]
Change the display mode for the specified molecules. Molecule names must be entered in PSL form. Valie display types are:

view molecule_name
Center he global view about the input molecule. The molecule name must be specified in PSL form. Only one molecule is required. If more than one is input, only the first is used.

visible molecule_name[s] on|off
Change the visibility of the specified molecules. Molecule names must be entered in PSL form.

scale factor
Scale the global view by a given factor.

labels molecule_name[s] on|off
Change the visibility of atom labels within the specified molecules. Molecule names must be entered in PSL form.