VMD  --- start of VMD description block
Name:
 SSCacheBunch
Synopsis:
 Automatically stores secondary structure information for animations with tweaked performance
Version:
 1.0
Uses VMD version:
 1.1
Ease of use:
 2
Procedures:
 
start_sscache molid - start caching the given molecule
 
stop_sscache molid - stop caching
 
reset_sscache - reset the cache
 
sscache - internal function used by trace
Description:
 Calculates and stores the secondary structure assignment for 
 each timestep.  This lets you see how the secondary structure
 changes over a trajectory.
 

 It is turned on with the command "start_sscache> followed by the
 molecule number of the molecule whose secondary structure should be
 saved (the default is "top", which gets converted to the correct
 molecule index).  Whenever the frame for that molecule changes, the
 procedure "sscache" is called.
 

   "sscache" is the heart of the script.  It checks if a secondary
 structure definition for the given molecule number and frame already
 exists in the Tcl array sscache_data(molecule,frame).  If so, it uses
 the data to redefine the "structure" keyword values (but only for
 the protein residues).  If not, it calls the secondary structure
 routine to evaluate the secondary structure based on the new
 coordinates.  The results are saved in the sscache_data array.
 

 Once the secondary structure values are saved, the molecule can be
 animated rather quickly and the updates can be controlled by the
 animate form.
 

  To turn off the trace, use the command "stop_sscache", which
 also takes the molecule number.  There must be one "stop_sscache"
 for each "start_sscache".  The command "clear_sscache" resets
 the saved secondary structure data for all the molecules and all the
 frames.
 

Performance tweak SSCACHEBUNCH (linux only)
 Frames are computed in a forward bunch to save TCL "exec" calls which
 are the time consuming factor, not STRIDE.
 Use env(SSCACHEBUNCH) to control how many frames are computed at once.
 Multiple thousands are possible for BUNCH value, only limit is hard disk space.
 1st play of trajectory shoulnd't be reverse direction of course.
Files: 
 sscachebunch.tcl
See also:
 the VMD user's guide
Author: 
 Andrew Dalke <dalke@ks.uiuc.edu>
 Norman Geist norman.geist@uni-greifswald.de
Url: 
 http://www.ks.uiuc.edu/Research/vmd/script_library/sscachebunch/