VMD User's Guide
VMD User's Guide
VMD User's Guide
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Hot Key Command Purposer, R mouse mode 0 0 enter rotate mode; stop rotationt, T mouse mode 1 0 enter translate modes, S mouse mode 2 0 enter scaling mode0 mouse mode 4 0 query itemc mouse mode 4 1 assign rotation center1 mouse mode 4 2 pick atom2 mouse mode 4 3 pick bond (2 atoms)3 mouse mode 4 4 pick angle (3 atoms)4 mouse mode 4 5 pick dihedral (4 atoms)5 mouse mode 4 6 move atom6 mouse mode 4 7 move residue7 mouse mode 4 8 move fragment8 mouse mode 4 9 move molecule9 mouse mode 4 13 move highlighted rep% mouse mode 4 10 apply force on atom∧mouse mode 4 11 apply force on residue& mouse mode 4 12 apply force on fragmentTable 4.1: Mouse control hot keys.4.2 Using the Spaceball in the Graphics Window<strong>VMD</strong> provides optional support for Spaceball six-degree-of-freedom input devices. The Spaceballmay be used to rotate, translate, and scale molecules, using up to 6 control axes simultaneously (3axes in translation, 3 in rotation). The Spaceball can be used independently and simultaneouslywith the mouse. With the spaceball in one hand and the mouse in the other, a user can performcomplex picking and identification operations more efficiently, since the mouse can be left in pickmode (for example) while the Spaceball is used to perform rotations, translations, and scalingoperations with the other hand.The Spaceball can be run in one of several modes within <strong>VMD</strong>. The Spaceball interface currentlyprovides two methods of rotation and translation, and a scaling mode. The Spaceball interfacecurrently uses Button 1 (known as Function 1 in the SpaceWare driver) to reset the view, andButton 2 to cycle through the available Spaceball interface modes.4.2.1 Spaceball Driver<strong>VMD</strong> interfaces to the Spaceball in one of two ways; either by communicating directly with theSpaceball using built-in serial interface software, or vendor provided drivers. Unix and Mac OS Xversions of <strong>VMD</strong> use the built-in serial Spaceball driver. At startup, <strong>VMD</strong> checks for the existenceof an environment variable <strong>VMD</strong>SPACEBALLPORT. This environment variable must be set tothe Unix device name of the serial port to which the Spaceball is attached. The serial port devicepermissions must be set to allow the <strong>VMD</strong> user to open the device for reading and writing. Intypical usage, this usually requires performing a chmod 666 /dev/somettyname on the appropriatedevice as root. One restriction with the use of the built-in Spaceball driver is that only one <strong>VMD</strong>process may safely use the Spaceball at a time. If multiple <strong>VMD</strong> sessions are started on the samemachine and all are set to open the Spaceball, it will behave very erratically.27