Overview of MDFF commands

At present, all MDFF commands in VMD are available only through the Tcl command-line interface. You can use the text console called Tk Console to enter commands. You can also use the VMD prompt in the text console window. This window normally contains the prompt vmd >. For simplicity, in this tutorial we use several VMD text commands (not specific to MDFF) that are also available via the graphical interface.

1

Start a new VMD session. In the VMD Main menu select Extensions $\rightarrow$ Tk Console to open the VMD TkConsole window (Fig. 1). You can now start entering Tcl/Tk commands here.

Figure 1: The VMD Tk Console window.

2

In order to use MDFF commands, you first need to load the MDFF package. This can be done by entering the following command in the Tk Console window:

package require mdff

3

Throughout the tutorial we assume that MDFF commands have been enabled by running the command above. You can add the line above to your VMD startup file .vmdrc or vmd.rc in Unix or Windows, respectively. The VMD startup file is typically located in the user's home directory. Check the VMD user guide for more information.

4

Type mdff to see a list of available MDFF commands. The following information should be printed in the console:

Usage: mdff <command> [args...]
Commands:
  ccc        -- calculates the cross-correlation coefficient
  check      -- monitors the fitting via RMSD and CCC
  constrain  -- creates a pdb file for restraining atoms
  delete     -- deletes volume corresponding to atomic structure
  edges      -- creates a map with smooth edges
  fix        -- creates a pdb file for fixing atoms
  griddx     -- creates a map for docking
  gridpdb    -- creates a pdb file with atomic masses in the 
                beta field
  setup      -- writes a NAMD configuration file for MDFF
  sim        -- creates a simulated map from an atomic structure

5

You can type any command to obtain its usage information. For example, type mdff sim to check the syntax of the command that generates a simulated map from an atomic structure. We will cover most MDFF commands throughout the tutorial.

WARNING: The MDFF software is considered experimental and the syntax of commands described in this tutorial is subject to change.