Copyright (C) 2001 Tommi Hassinen.

1. Table of Contents

2. Introduction

By different "components" of the program we mean the set of different "projects" that the program supports. By a "project" we mean the corresponding molecular model, and some additional information that may be linked to the molecular model. At the moment projects are supported for quantum mechanics and molecular mechanics, and a project for reduced protein models is under development.

Inside these different "components" of the program, there is an another layer of organization. We use the term "model" to describe the contents of our molecular model, for example a set of atoms and bonds. For the mathematical expressions and computer code that gives the description of our model, we have a term "engine". There can be many different "engines" available for a single "model"; for example we may have many different molecular mechanics force fields implemented which we can use to describe our molecular mechanics model. Finally, we have a set of algorithms that we can use to modify or study our model; for example we can use geometry optimization or molecular dynamics algorithms with our favourite computation "engine" to study our models.

2.1. The main user interface elements

The items in the main menu cover the features:

- File : Create new projects, Open projects from files, Exit the program.
- Windows : Change the GNOME MDI mode settings from the system defaults, a list of currently open project files.
- Help : Display the About Box and this User's Manual.

The buttons in the toolbar are mouse tool buttons. One of these buttons is always pressed down, and this determines what operations are done when the user handles the models with mouse. The left mousebutton always triggers the mouse tool operations, and the tools and operations are the following:

- Draw : Add atoms or bonds to the model, or change the types of existing atoms or bonds in the model.
- Erase : Remove atoms or bonds from the model.
- Select : Mark atoms selected in the model. Selecting an already selected atom will de-select it.
- Zoom : Change the zooming of this 3D-view.
- Translate tools: Translate the "camera" which produces this 3D-view.
- Orbit tools: Orbit the "camera" which produces this 3D-view around it's focus point. Practically this means that you can rotate the molecules in your 3D-view using these tools.
- Rotate tools : Turn the "camera" which produces this 3D-view. Practically this is means that you "turn your head" in the 3D-landscape that consists of the system you study. Use these tools with caution; you might easily "lost" your system if it's a single molecule.

In addition to these standard features some of the tools have some special features:

- Select : The selection tool can, in addition to atoms, select objects (for example: spotlights, color planes and color surfaces) that are rendered as opaque (non-transparent) objects. In order to select transparent or invisible objects, you have to use the "treelist view" (under construction).
- Translate tools and Orbit tools: These tools work differently if you hold down the modifier key SHIFT before you use the tool. In this case the tool affects not to the "camera" but to the currently selected object or to the currently selected set of atoms in the model. Using the SHIFT key and these tools you can translate and/or rotate the objects or atoms/molecules in the model. In addition to the SHIFT modifier key, the Translate tools have an another modifier key CTRL. This makes the tool use the object's internal coordinate axis in the translation instead of the camera's coordinate axis. Therefore, by using the key combination SHIFT+CTRL with the Translate Z tool, you can easily "scan" your model using a color plane object.

2.2. Additional tips and tricks

- In all 3D-views, the right mouse button will display a popup-menu. These popup-menus can be different in different types of models, making different features available in different models (for example, molecular mechanics models have different features available than quantum-mechanical models).
- There is a status bar visible in the program, but it's not very actively used yet. Many parts of the program do still their output to the console window where the program was started. We are working on this, but it's going to take some time before all these things are fixed. So, in the meantime you are adviced to start the program from a console window, and to keep that console window visible. Sometimes you even might be asked for input in the console window!
- You are adviced to use the "Notebook" MDI mode of GNOME to make the handling of multiple documents as easy as possible.
- The main menu and the toolbar support a "drag and drop" feature: just click the "handle" of the menu or toolbar using left mouse button, "drag" it outside the main window, and "drop" it to suitable place.
- The "volume rendering" object is different from all other objects because it is connected to a "camera", and actively orients itself to this camera each time the camera is translated or rotated.

3. Quantum Mechanics Project - qm1gp

Currently we have no working QM engine of our own, but we use code "borrowed" from the MPQC program instead. In order to use any of the QM features, you have to compile and install the MQPC program to your system, and recompile the Ghemical program with the MPQC front-end feature enabled. This brings the working MPQC engine available, in addition to the default non-functional dummy engine. The MPQC engine just runs the MPQC closed-shell hartree-fock code, with STO3G basis set and no symmetry. Currently there are no algorithms available.

Currently the QM and MM models are difficult to use together; we are working for an improvement in this. Currently you are adviced to make your model as MM model, to save it, and to open it as QM model.

The popup menu in a "qm1gp" model currently has the following features:

- File : Import a "mm1gp" project, Close the project.
- Settings : Change the current element.
- Render : Add/remove views/lights. Change the rendering mode and projection.
- Objects : Add visualization objects (planes, surfaces etc) and remove them.
- Compute : Compute energy and prepare the model for above visualization options.
- Set Current Orbital : Here you can set the orbital index for visualization.

4. Molecular Mechanics Project - mm1gp

Currently we have an experimental Tripos 5.2-based molecular mechanics force field available for organic molecules. This force field is not tested or validated in any way, but it seems to produce reasonable geometries for organic molecules. There is also a variant of this engine for periodic systems (minimum image model); it seems to produce stable MD trajectories for molecules in a gaseous phase. Algorithms for geometry optimization and molecular dynamics are available.

The popup menu in a "mm1gp" model currently has the following features:

- File : Open and save projects, many file import/export options, close the project.
- Select : Select all, invert selection.
- Settings : Change the current element and/or bond type.
- Render : Add/remove views/lights. Change the rendering mode and projection. Add the treelist view (under construction).
- Objects : Add visualization objects (planes, surfaces etc) and remove them.
- Compute : Select the engine, compute energy, geometry optimization, molecular dynamics.
- MD trajectory viewer : Display saved molecular dynamics trajectories.
- Build : Add/remove hydrogens, sequence builder for amino/nucleic acids, center this 3D view.

5. Reduced Protein Modelling Project - mm2gp