I have a trajectory (.xtd) of a system with interesting bits and a bunch of solvent. I want to delete the solvent molecules and animate the trajectory of what is left. I have written a script (stealing liberally from others here) that seems to do the deleting, but when I'm done, I can't animate the trajectory. In addition, I'd like to do the deletions on a *copy* of my original trajectory so that I don't destroy the original one.  How do I properly make a copy of a trajectory (giving it a new name) and how do I delete molecules within that trajectory and still animate it?  Thanks. I can't say that I understand the relationship between .xtd, .trj, and .msi or whatever files, so some of my problem likely lies there. Here are re relevant pieces of my script so far:

my \\\$xtd = "my_test";  # Name of the trajectory
my \\\$solvent = "Sketch 16"; # Set name given to the molecule
my \\\$start_frame = 1;  # Starting frame
my \\\$interval = 1;  # Extraction interval from the trajectory

#############################################################################

# Initialize

my \\\$doc = \\\$Documents{"\\\$xtd.xtd"};
print "Document: \\\$xtd.xtd\\n";
my \\\$number_of_frames = \\\$doc->Trajectory->NumFrames;
print "Number of frames = \\\$number_of_frames \\n";

###########################################################################
# Go through frames as instructed, delete the molecule

for (my \\\$frame_counter = \\\$start_frame; \\\$frame_counter <=\\\$number_of_frames; \\\$frame_counter = \\\$frame_counter + \\\$interval) {

print "Deleting \\\$solvent from frame \\\$frame_counter\\n";

for my \\\$molecule (@{\\\$doc->UnitCell->Molecules}) {
     if ((\\\$molecule->Name eq \\\$solvent)) { \\\$molecule->Delete;}
}

}

print "Deletion complete\\n";