User:Remig/plico/toabManual
Plico ToAlphBeta Jmol script manual
ToAlphBeta is a script of the Plico suite described here. It allows the user to change one section of a polypeptide from alpha helix to beta strand and vice versa or individual amino acids among the alpha, beta and L forms. The script can be found here. Copy and paste it to a text editor and save it as toAlphBeta.spt in your scripts location. The text "<SCRIPT_PATH>" should be replaced with the path to your scripts so that the required helper script tug.spt described here can be preloaded if needed.
It can then be launched by the following macro:
Title=PLICO To Alpha/Beta Script=script <path to scripts>/toAlphaBeta.spt;plicoToab
(Macros are placed in the .jmol/macros folder as described here.)
Operation:
Before invoking ToAlphBeta, a polypeptide would normally be already loaded in the application. When To Alpha/Beta is selected from the macro menu, a list of mouse actions appears in the upper-left of the Jmol application window.
Initially the only options are to ALT-CLICK on an atom to mark the block or side-chain to be moved or rotated, SHIFT-CLICK to rotate an amino acid to beta form, ALT-SHIFT-CLICK to rotate an amino acid to alpha form, ALT-CTRL-CLICK to rotate an amino acid to L form, and DOUBLE-CLICK to exit ToAlphaBeta. Press the left mouse button (if more than one) while holding down the ALT key or SHIFT key while hovering over an atom to perform these actions.
When a single amino acid is rotate to alpha, beta, or L form, its colors become highlighted and the chain N-ward of the amino acid moves to accommodate the change. The dihedral angles used are as follows:
alpha beta L phi -50 -100 50 psi -45 135 45
When ALT-CLICK is pressed on any atom, the list is expanded to include ALT-DRAG to move atoms, SHIFT-CLICK to set anchors, ALT-DRAG to move and SHIFT-ALT-DRAG to alt move.
Alpha/Beta mode:
When ALT-CLICK is pressed on a back-bone atom (or a CB atom), its residue is presented in the RASMOL color scheme* and halos are drawn on its N and C atoms to mark it as available to be rotated by ALT-DRAG. ALT-CLICK on a back-bone atom of another residue will then highlight all atoms between the two residues inclusive. The entire block will then be available to be rotated by ALT-DRAG or SHIFT-ALT-DRAG. When ALT-DRAG is performed by pressing the left mouse button down while holding the alt key down and then moving the mouse rightward, the selected block transitions from alpha helix to beta strand. If the mouse is move leftward, the selected block transitions from beta strand to alpha helix. During the drag, the menu background will go pink when collisions are present.
Anchors may be set on either side of the back-bone block with SHIFT-CLICK to restrict the range of phi and psi bonds available to accommodate movements. Anchor atoms are haloed. A C-terminal anchor (C-ward) is set by default at the N of the C-terminal residue though it can then be moved or removed if desired. When a back-bone block is moved, atoms beyond the anchors are then guaranteed not to move as their psi and phi bonds are not rotated. (The N-terminal side of the block beyond any N side anchor (N-ward) may nevertheless see some small movement in certain collision cases. )
If no anchor has been set towards the N-terminal of the polypeptide (the usual case), any polypeptide Nward of the block moves along with block. Otherwise the Nward polypeptide remains stationary until the drag is completed and then is adjusted in the same way as described in the Tug manual. If the action cannot be accommodated, you are given the opportunity to restore the chain to its previous state.
The principal use of Alpha/Beta is to convert a stretch of the emerging alpha helix to beta strand where any polypeptide Nward of the stretch moves freely, rotating as helix unwinds. In such cases no Nward anchor would be set.
SHIFT-ALT-DRAG behaves like ALT-DRAG except that movement is directed Cward of the block instead of Nward. If the Cward anchor is removed, any polypeptide Cward of the block moves freely with the block.
Side-chain mode:
When ALT-CLICK is pressed on a side-chain atom beyond the CB atom, a circle is drawn around the atom and subsequent movements are then restricted to the side-chain until ALT-CLICK is pressed again on the same or another atom. ALT-DRAG then pulls just the side-chain in the direction of mouse movement as allowed by rotation on the chi bonds of the side-chain with no collisions. ALT-SHIFT-DRAG does allow collisions should that prove necessary. Rotation angles are restricted to multiples of 60°. Pulling on the CG atom of proline toggles between its two puckered states. Note that marking a side chain atom does not cancel back-bone selection.
When ALT-CLICK is pressed on a back-bone O atom, a circle is drawn around the atom and subsequent movements are then restricted to that atom until ALT-CLICK is pressed again on the same or another atom. ALT-DRAG then rotates the phi and psi bonds on either side of the O in opposite directions to move the O atom with minor movement of the atoms in the N-terminal direction from the O atom. SHIFT-ALT-DRAG does the same except the minor movement is of the atoms in the C-terminal direction from the O atom. Note again that marking a back-bone O atom does not cancel back-bone selection.
