The Plico suite was designed to support modeling the de novo protein folding approach where folding is envisioned to occur as the polypeptide emerges from the ribosome as water and side-chain oxygens (predominantly) disrupt the h-bonds of the alpha helix (likewise for RNA emerging from polymerase).
The suite consists of Jmol scripts for manipulating polypeptides, scripts for manipulating polynucleotides and scripts for manipulating either. The names of scripts for polynucleotides generally end in NT (except for the script "polymeraze.spt"). Scripts designed for both polypeptides and polynucleotides include "modify.spt" and "convert_residue.spt".
The scripts can be run manually or as macros in the Jmol application. In the future I may also provide means to add them to the Jmol menu.
When run, the scripts either prompt for inputs or else display a list of available mouse actions as echo text in the upper left corner of the Jmol window. These actions consist of mouse clicks and drags in combination with the modifier keys SHIFT, ALT and CTRL. The list of actions is presented with a yellow background. When the script is busy for any time, the background changes to pink until the script action completes. Clicking on the top line of the list will toggle the list display on and off should the list get in the way.
Some scripts present a menu with a gray background. Clicking on the menu item then selects the action. Clicking on the top line of the menu will toggle the menu display on and off should the menu get in the way.
All scripts should be exited with SHIFT-DOUBLE clicking.