Bridging Waters 1.0
REQUIREMENTS: VMD Version 1.0 or greater
When the frame changes, a cache is checked to see if a selection has been
computed for it. If not, one is made and added to the cache. The Tcl
variable "bridging" is set to the atomselection, and element 0 of the
graphics list is changed to "@bridging". This forces that element to
be redrawn using the new selection.
HOW IT WORKS:
One of the researchers here needed a way to see which waters bridged
between a protein and a nucleic acid during a trajectory. The
specific waters change during the simulation, so the static method
used in the graphics form doesn't work. Instead, the vmd_frame
variable and a caching method similar to the sscache of the previous
section was used for the following solution:
The cache data is stored in the array bridging_waters. Unlike
sscache, this array is indexed only by the frame number; you'll
have to modify it to analyze multiple changing selections.
When the frame number changes, the cache is checked and, if no data
exists, the selection is rebuilt. Since the selection is created in a
procedure, it must be given by the global command to make it exist
outside that procedure's context.
The global Tcl variable bridging is set to the selection for
The first text selection in the graphics form is set to
@bridging. This is one of the special extensions to the selection
language which enable the selections to reference a Tcl variable.
Note also that the display updates are temporarily turned off. This
is used to keep the display from being drawn an additional time by the
call to mol modselect. This is done every time the frame
changes since that's the only way to tell VMD the graphics have
changed; forcing it to recalculate that representation's display.
Since the selections are available in the global scope, you can analyze
the results at any time. The num_bridging function prints how many
atoms are in each selection of the cache.
start_bridging molid -- start the trace on the vmd_frame for molid
stop_bridging -- stop the current trace
calc_bridging -- check the cache, create a selection if needed
num_bridging -- example of how to get data from the cache
mol load psf er-ere.psf pdb er-ere.pdb
# start the bridge calculations
# however, one frame has already been read, so do its calculations
# by hand
# read the rest of the frames (the selections are automatically computed)
animate read dcd dyn100frames.DCD
DOWNLOAD THE FILE:
Andrew Dalke (email@example.com)