DNA demos for VMD

REQUIREMENTS: VMD Version 1.7.1 or newer 

        These are a collection of VMD demos donated by
        Alexander Balaeff.


  Alexander Balaeff sure@ks.uiuc.edu

From the README file included with the demos

The scripts set up a menu to present the protein-DNA complex
of the lac repressor, solvated in a water bath, with different 
elastic rod loops attached to the protein-bound DNA segments.
Two of those solutions (the short loops) are animated, the 
animations showing different steps of solving the elastic rod
equations.  The other four solutions (the long loops) are static, 
showing only one final structure of the elastic rod. On top of 
the elastic rods, one shows fitted all-atom DNA structures, 
electric field profiles, forces of protein-DNA interaction, 
and the CAP protein bound within the short loops.


The kit contains the scripts:


and is located in the directory /home/sure/Demos/Complete_2002 .
To see how the scripts work, go to that directory, and start
the main presentation:  vmd -e present.tcl


The main directory contains the TcL scripts, UNIX utility scripts
for file copying, etc., the PSF files for the presented molecules,
the PDB files for the lac repressor and the water bath, and the
BMP icons for the menu panels.

Six subdirectories:  Short_{1,0} and Long_{Up+1,Up_0,Down-1,Down_0}
contain the PDB data for the molecular sets of elastic rod solutions 
and their accessories: all-atom DNA, forces, electric fields, and 
CAP structures; UNIX utility scripts, and, in case of the animated 
loops, the scenario scripts Scenario.tcl.


The control of the presentation is condensed into one Tk menu panel.
The menu includes 

(a) a toggler to swith on and off various sites in the all-atom DNA 

(b) buttons to turn on and off the lac repressor and its water bath, 

(c) two sets of controls for the animated molecular loops, including 
the buttons to turn on/off the loops and each of their accessories
(all-atom DNA, CAP, electric field, protein-DNA interaction force),
the buttons to run through the animation of solving the elastic rod
problem, and the main button which turns on and off the whole 
molecular set,

(d) a panel that toggles on/off the long (static) loops and their
accessories: four smaller versions of button sets described in (c)
are organized into a single table.


present.tcl  --  the master script, which sets up sets up the VMD 
presentation styles and colors, loads lac repressor + water, calls 
the other scripts (which create the Tk menus and load the PDB data 
for the elastic loop molecular sets), and resets the presentation
to its initial state.

main_panel.tcl  --  creates buttons and areas of the main menu panel,
defines procedures for the DNA site toggler and the lac repressor/water
buttons (menu areas (a) and (b), as above).

load_set.tcl  --  contains a TcL procedure that loads an animated
molecular set from a given subdirectory (e.g., Short_{1,0}) and
sets up its Tk menu controls (menu area (c), as above).

set_procedures.tcl  --  contains TcL procedures called by the buttons
of the animated set menus (those created by the load_set.tcl).

static_rod_panel.tcl --  sets up the Tk panel (menu area (d), as above) 
for turning on and off the components of the static loops.

load_static_set.tcl  --  contatins a TcL procedure that loads 
a static molecular set from a given subdirectory (e.g., Long_*) 
and fills up the pre-defined area of the main menu (allocated by 
static_rod_panel.tcl) with Tk menu controls for the loaded set.

Scenario.tcl  --  defines the animation scenario for an animated
elastic loop molecular set.  A "scenario" consists of "animation 
states" in which each molecule of the set (the rod, all-atom DNA, 
etc.) occupies a certain frame of its pre-loaded trajectory.
The buttons of the menu panel (c) move the molecular sets through
its animation states, much like the VMD animation buttons do.
The file Scenario.tcl does not have to exist: if no such file
is found in the sub-directory from which an animated set is loaded,
then a default scenario is arranged that simply goes through the 
loaded trajectories step-by-step until the end is reached. 

That is the whole story: more comments can be found within the
scripts themselves. Enjoy! I keep adding data to the presentation 
so at each particular moment when you run the demo, the data for 
various accessories of the elastic rod sets may not match each other 
very well.  However, the data organization is going to be the same 
and no major revision of the presentation scripts is planned.

                                  -- Alexander Balaeff, 5/1/2002.