User:Remig/plico/tugManual
Plico Tug Jmol script manual
Tug is the central script of the Plico suite described here User:Remig/plico and is loaded by many of the other scripts if not already in place. It allows the user to move or rotate one section of a polypeptide against another by mouse actions. The script can be found here User:Remig/plico/tug. Copy and paste it to a text editor and save it as tug.spt in your scripts location.
It can then be launched by the following macro:
Title=PLICO Tug Script=script <path to scripts>/tug.spt;plicotug
(Macros are placed in the .jmol/macros folder as described here Macro.)
Operation:
Before invoking Tug, a polypeptide would normally be already loaded in the application. Any hydrogens should have been deleted as well as any alternate atoms. Residues must be labeled (no UNKs please). The Plico script Remap can be run if residues are not labeled as would be the case if the polypeptide was loaded from an XYZ file. However, if the polypeptide was generated by the Plico script Polymeraze, no other action would be required. The ball-and-stick style scheme, perhaps with dots on, seems best for working with tug.
When Tug is selected from the macro menu, a list of mouse actions appears in the upper-left of the Jmol application window.
Initially the only Tug option is to ALT-CLICK on an atom to mark the block or side-chain to be moved or rotated. Press the left mouse button (if more than one) while holding down the ALT key while hovering over an atom to perform this action.
When ALT-CLICK is pressed on any atom, the list is expanded to include ALT-DRAG to move atoms, SHIFT to set anchors, ALT-CTRL to set pivot points, ALT-SHIFT to set a destination atom, and DOUBLE-CLICK to exit Tug.
When ALT-CLICK is pressed on a back-bone atom (or a CB or O 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 moved or 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 moved or rotated by ALT-DRAG.
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. 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-DRAG is performed by pressing the left mouse button down while holding the alt key down and then moving the mouse, just the selected back-bone or side-chain moves accordingly. For a back-bone selection, when the button is released, the chain on either end of the selection is then rebuilt to proper bond lengths and angles by rotation on available phi and psi bonds. The required processing can take some time and the menu background color will go from yellow to pink for the duration. If the action cannot be accommodated, the chain will be restored to its previous state. Sometimes Jmol fails to recognize the button up event; in that case simply do another drag away and back.
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 highlighted in RASMOL colors*. 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. ) Note that some psi and phi bonds may be made unavailable regardless of anchor placement by action of the Plico Freeze script.
One or two pivot points may be set with ALT-CTRL-CLICK on any atom. Pivot point atoms are colored green. When a single pivot point is set, the back-bone selection rotates on the pivot rather than translating. The rotation is in the XY viewing plane. When two pivot points are set, the rotation is instead on the axis between them.
A single atom may be set as a target with ALT-SHIFT-CLICK. A cross will appear on the atom when so selected (and will disappear if ALT-SHIFT-CLICK is done on the same atom.) When a target atom is selected, mouse drag movements, including rotations, then move towards or away from the target atom. Otherwise movements are in the XY viewing plane.
When DOUBLE-CLICK is performed anywhere, a prompt is presented allowing you to exit Tug keeping your changes if any, to cancel and go back to Tug, or to undo the entire Tug session and restore the polypeptide from the file, tugsave.pdb, created when Tug was first entered.
Performance:
Tug is written as a compromise between performance and robustness. It makes heavy demands on Jmol resources and Jmol sometimes responds by locking up, requiring the services of the task manager to close it down. If that happens, you can then restart Jmol and load the file tugsave.pdb to quickly recover. Regardless movements in Tug are better made in several small steps rather than one large step. Large movements can better be achieved with other scripts in the Plico suite such as Turn, ToAlpha, and ToBeta.
Performance is achieved by only moving the selected block when dragging and only checking for collisions within the atom set between anchors after the chain has been rebuilt. Collisions of the selected block with atoms outside the atom set between anchors stop movement only if the collision is with a back-bone atom or a side-chain atom that cannot be moved away. Water molecules are deleted when encountered but may be replaced later by the Plico script Hydrate.
After the chain is rebuilt, internal collisions are resolved by moving side-chains, deleting water, and counter-rotating back-bone oxygens. The planar nature of the peptide bond results in the phi and psi bond pair on either side of a back-bone oxygen being parallel. Therefore rotations on both, identical in magnitude but opposite in direction, result in substantial movement of the oxygen away from a collision situation without much consequent movement of the rest of the molecule. Some movement does nevertheless occur and Tug can sometimes move the entire chain N-ward of the oxygen somewhat despite an N-ward anchor.
If collisions cannot be resolved, Tug restores the previous state. Also when exiting Tug, you are given the option to undo the entire session.
- If the default color scheme is RASMOL then the JMOL colors are used for highlighting.
