Features of and Help with IMIMOL

Features of and Help with IMIMOL.

Current Features of IMIMOL.

There is a canvas where atoms can be placed by clicking, and bonds between them can be defined by dragging. The geometry on the canvas is completely adjustable, and has no intrinsic relation to the geometry in space of the molecule described. One must omit bonds from covalently bound rings so that one obtains the atom/bond tree.
The program automatically generates the line graph of the atom/bond tree, and the user selects certain edges of this line graph to be deleted so that one obtains the bond/angle tree. The line graph of this tree is automatically generated as well, and the user again selects the edges of the line graph to be deleted so that one obtains the angle/wedge tree. The orientations of improper wedges can be switched from the default.
Various levels of detail can be displayed or hidden. The atom names are hierarchical: ``O.His.129.A'' might be the name of the Oxygen attached to the backbone in the residue Histidine 129 in the A chain of some protein. Annotations can be attached to the canvas, and their position, boldness, and size can be changed.
Gluing of two Z-systems at sites (A0,A1,A2) and (B0,B1,B2) can be accomplished in ``merge'' mode in two steps. First drag and drop A1 onto the leaf atom B0; B0 will then be destroyed and replaced by A1. Then drag and drop B1 onto the leaf atom A0; A0 will then be destroyed and replaced by B1. The new wedge [A2,A1,B1,B2] must be added to the angle/wedge tree by double clicking on its ghost.
To assign coordinates one clicks on a bond, angle, or wedge, and edits the value (of type `string') in the property box.
A root site can be defined by clicking on an atom, a bond containing it, and an angle containing it.
Z-systems can be exported in an IMIMOL readable (ascii) format which can then be imported into other Z-systems. A rooted Z-system can be exported as a Z-matrix and viewed using various molecular visualization programs, such as RASMOL. Gaussian-style Z-matrices are exported in a very readable manner, where the atoms are ordered according to the hierarchy intrinsic to the atom names. A picture of the canvas can be exported as a color postscript file (you might want to first change the background color to white).
Various facilities for building large Z-systems are included such as panning (translating the Z-system on the canvas), zooming in or out, focussing on a part of a Z-system, recentering the molecule, rotating, reflecting, etc.
XYZ coordinates from structure files available on the internet can be imposed on a Z-system for the same molecule, essentially accomplishing a conversion from Cartesian to (user defined!) internal coordinates. Likewise the XYZ coordinates of a (numerically) labeled and rooted Z-system can be exported to a file, and then imposed on a new Z-system for the same molecule, accomplishing a conversion from one internal coordinate system to another.
One can also define an alternate site (besides the root site) and export a MAPLE procedure file which computes symbolically the 4x4 coordinate transformation matrix from the root system to the alternate system. This feature is extremely useful for studying complex geometric questions about molecular conformations.
A console window displays error and other messages. For brief explanations of commands use the help pulldown menu.

Features of Future Versions of IMIMOL.

Scripting language for all IMIMOL functions to allow automation of large molecule construction.
Exporting .DCD files. This feature allows one to make movies of arbitrary motions of a molecular system, which can then be viewed using VMD. Certain bonds, angles and/or wedges are labelled with special strings "=variablename" indicating that the numerical values for these labels are to be read from a file.
Implementation of the GZ-system formalism, i.e. components, linkages, hierarchy, detail hiding, construction and manipulation by icon, etc..
Automatic generation of kinetic and potential energy, as well as initial condition, specifications for molecular dynamics simulations in internal coordinates. (?)
Contact mapping between surfaces in multi-component complexes.

Help with IMIMOL. (Under construction!)

To add a previously stored molecule to your current construction under the File menu select "Add from file...". Enter the file name and press OK. The inserted structure appears with all its atoms selected, but the program is in Add Atom Mode. If you wish to reposition the inserted structure, first enter Select Atom Mode. Then click and hold the left mouse button and drag to the position you want, and then release the mouse button. If you wish to rotate the selected structure click and hold the right mouse button and drag it horizontally; release the mouse button when it is in the orientation you want. To reflect the inserted structure about a horizontal line, press the "Flip" button. To unselect this set of atoms left click anywhere on the canvas away from any atoms.
If one wishes to view the three dimensional shape of the current molecule one must choose a root site. To do this, first check under the View menu, Hide/Show submenu, to see that atoms, bonds, angles, and roots are visible. (If they are you should only see the hide atom, hide bond, hide angle, and hide root options.) Then enter Root Tree/Atom mode and left click on the root atom. It should then be highlighted. Then enter Root Tree/Bond mode and left click on the root bond (which must be incident on the root atom). It should then be highlighted. Then enter Root Tree/Angle mode and left click on the root angle (which must be incident on the root bond). It should then also be highlighted.
If you wish to use the Export Maple Procedure option under the File menu then you must define an alternate root. This is done exactly like defining the root except one must hold down the shift key when one is left clicking on the alternate root atom or bond or angle.