Desmond Tutorial

Analyzing Trajectories Using VMD
Getting information about snapshots
• frame; default -1. The frame is the index of the snapshot referenced by the selection.
The default value of -1 means that the selection should reference whatever the current
frame happens to be. A frame value of 0 or higher means the selection always
refers to the same frame, even if the current frame changes. If the frame referenced by
selection does not exist, then the last frame in the molecule is used.
You can get and set the frame attribute in the usual Python way:
n1 = len(wat0) # number of atoms in the selection
f = wat0.frame # returns -1
wat0.frame = 20 # makes wat0 reference frame 20
n2 = len(wat0) # will be equal to n1!
wat0.update() # recompute the selection based on frame 20
n3 = len(wat0) # might be different from n1
Note, however, that changing the frame does not cause the selection to be recomputed.
Only the update() method changes the set of atoms referenced by an existing selection.
However, changing the frame does change the result of calculations that depend on the
coordinates, such as center() and rmsd(). The reason things are done this way is
because one might want to select a set of atoms based on a distance criterion, such as the
wat0 selection in the example above, and then see howthe positions of those atoms
change over time. There would be no way to do this if changing the frame automatically
updated the selection.
With an atom selection object in hand, you can extract data about a molecule for the atoms
in the selection. Continuing from the first example:
# Get the number of alpha carbons
num_ca = len(ca)
# get the residue name of each alpha carbon
resnames = ca.get('resname')
# Set the 'type' attribute of all atoms to 'X'
all.set('type', 'X')
# Compute the center of mass the protein atoms in frame 10
mass = pro10.get('mass')
com = pro10.center(mass)
# Align pro10 to the corresponding atoms in frame 0, and compute
# the RMSD relative to frame 0.
pro0 = atomsel('protein', frame=0)
m = pro10.fit(pro0, weight=mass)
pro10.move(m)
rms = pro10.fit(pro0)
Snapshots
Time‐varying data in VMD includes positions, velocities, and periodic cell parameters.
The atom selection interface can be used to extract positions and velocities from a given
frame in the same way as other attributes:
# get the x, y, and z coordinates for the atoms in wat1 as Python lists
x = wat1.get('x')
y = wat1.get('y')
September 2008 D. E. Shaw Research 91