Desmond Tutorial

Desmond Tutorial
Analyzing Trajectories Using VMD
Figure 9.2 Loading files from the GUI
Click Browse and select
your structure file.
Choose the type of
Maestro file you want to
load and click the Load
button.
Figure 9.3 Loading files from the GUI
Select the ‘clickme.dtr’ file
to load the frames within
the directory containing the
‘clickme’ file.
At this point, you may wish to limit the number of snapshots that are loaded from the
trajectory. If you havenʹt done so already, choose Desmond Trajectory from the file type
chooser. The Frames box underneath should now be active. Type in values for the snapshots
you want to load. The default First value of 0 corresponds to the first snapshot in
the trajectory; the default Last value of —1 corresponds to the last snapshot; and a Stride
of 1 means load every snapshot in the selected range. Choosing a Stride of 10 would load
every 10th snapshot from the trajectory.
You also have the choice of Load in background, which is slower but keeps VMD responsive
during the load and gives you the option of canceling the load before it completes,
and Load all at once, which is quite a bit faster but leaves VMD in an unresponsive state
until the load has completed. Use Load all at once whenever youʹre reasonable sure that
all the frames youʹre about to load will fit in memory.
Loading files from the scripting interface
Files can also be loaded into VMD using the Tcl or Python scripting interface. Weʹll confine
ourselves here to the Python interface, although you may find using the Tcl interface
with VMD TkCon window more convenient for simple tasks.
Load the molecule module by typing import molecule at the Python prompt. To load
a structure file and all frames of a trajectory file, enter the following commands:
import molecule
molid = molecule.read(molid=-1, filetype='mae', filename='structure.cms')
88 D. E. Shaw Research September 2008