Copyright (C) 2001-2002 Tommi Hassinen.

1. Table of Contents

 Appendix 1 : Using 1D and 2D Conformational Search Tools

2. Introduction

This document describes the user interface of the Ghemical for GNOME desktop environment, as well as the main features of different components of the program. Ghemical for GNOME is a standard GNOME MDI application, so the generic features of GNOME MDI applications and user interfaces apply to this program as well.

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 also exists but it still is a work-in-progress.

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.
- Measure : Measure distances, angles or torsions. Click a sequence of atoms (like with the Select tool) to define distance, angle or torsion.

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 "project view".
- 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.
- All different "views" of a project are grouped into a single "notebook" of the project; there is a separate "page" for each view. The 3D-graphics views can also be detached from this notebook; take a look at the "Views" section of the popup-menu. Using the "detach" option you can use multiple views simultaneously, which is otherwise difficult.
- 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 QM code of our own, but we use code "borrowed" from external programs MOPAC7 and MPQC instead. The code from MOPAC7 is included in the package, but the MPQC code is external (at the moment, at least). In order to use the features from MPQC program, you have to compile and install the MQPC program (the older version 1.2.5; the new version 2.0 is not yet supported) 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 MOPAC7 engine.

Select "Compute/Setup..." from the popup menu to check the settings for your calculation; hamiltonian / basis set to be used and total charge of the system. Only singlet states with even number of electrons are supported at the moment.

The MOPAC7 engine runs MOPAC7 code in cartesian coordinate (XYZ) mode. User can select one of the following hamiltonians: MNDO, MINDO/3, AM1, PM3. When using MOPAC7 engine please note the following:
    1) MOPAC7 code relies heavily on use of global variables, so it is not possible to run multiple instances of MOPAC7 at the same time in a same program; you have to start multiple programs at different working directories instead.
    2) The MOPAC7 engine creates intermediate files like FOR005 and SHUTDOWN to the working directory when run. In normal operation these files are removed when not needed anymore, but if something goes wrong you have to manually remove these files!
    3) Due to a bug in MOPAC7, the first three atoms should not be linearly arranged; this might affect for example carbon dioxide molecule O=C=O. When studying cases like this, draw the molecule in a sequence 1-3-2 instead of sequence 1-2-3 to avoid the problem.
    4) The hamiltonians in MOPAC7 support (at least?) the following elements: H, C, N, O, F, P, S, Cl, Br, I. If you try to use elements not supported by MOPAC7, the program will stop.

The MPQC engine runs the MPQC closed-shell hartree-fock code with no symmetry. User can select any of the standard ab initio basis sets from STO-3G to 6-31G**.

Both QM engines can run geometry optimization, and draw ESP, MO, and MO density plots. Also a specific energy-level diagram view is available that shows molecular orbital indices, energies (in eV) and occupation (you can use mouse tools Zoom and Translate XY to manipulate the diagram):

It is possible to convert MM models to QM models and vice versa. Therefore you are adviced to draw your molecule as a MM model, optimize it to get a good starting structure, and then to convert it into a QM model for further refinement and inspection. To save your QM model, you are adviced to convert it into MM model and then save it (currently there is no file format specified for QM models).

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. Add an energy-level diagram view.
- Objects : Add visualization objects (planes, surfaces etc) and remove them.
- Compute : Select the engine and other settings, compute energy, geometry optimization.
- Set Current Orbital : Here you can set the orbital index for visualization.
- Convert to MM project : Copies the contents of this project into a new MM project, and optionally closes this project.

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, molecular dynamics and conformational search 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.
- Objects : Add visualization objects (planes, surfaces etc) and remove them.
- Compute : Select the engine, compute energy, geometry optimization, molecular dynamics, random conformational search, 1D/2D conformational search.
- MD trajectory viewer : Display saved molecular dynamics trajectories.
- Build : Add/remove hydrogens, sequence builder for amino/nucleic acids, center this 3D view.
- Convert to QM project : Copies the contents of this project into a new QM project, and optionally closes this project.

5. Reduced Protein Modelling Project - mm2gp

Protein molecules are modelled using 1-3 "virtual atoms" per amino acid residue in this kind of model. Several chains and disulphide brides are supported, but non-natural amino acids are not. Files can be imported in the PDB file format. The force field is fully functional with an initial parameter set, and algorithms for geometry optimization and molecular dynamics are available.

There are no sophisticated tools for model building yet, but they might be coming later.

6. References