VMD  --- start of VMD description block
 Automatically stores secondary structure information for animations with tweaked performance
Uses VMD version:
Ease of use:
  • 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/