Welcome page and Program overview Tools and toolbars The Contextual menu and the Selection  The Display settings

MoProViewer Nice SplashScreen
                                                        DOCUMENTATION

MoProViewer is a molecular viewer dedicated to the charge density analysis field, linked to the MoPro refinement program suite and especially to the VMoPro program, which computes electron density derived properties. MoProViewer can be considered as a graphical interface to VMoPro as it allows to graphically configure a computation and to display the results. MoProViewer can display 3D isosurfaces, 2D isocontours maps, critical points and bond paths, electrostatic moments, gradient lines fields and topological basins.


This document

On this page can be found a short introduction to the program philosophy, a description of its main window, and the mouse buttons usage in the program. Next are informations about how to open files of various formats. At the bottom of the page, a list of current known bugs is given, as well as the current program limitations.


Introduction


MoProViewer allows displaying a molecule, from various file types such as MoPro, PDB, CIF etc…, and to compute with the help of the VMoPro software properties related to the charge density modelling (static or dynamic electron densities, electrostatic potentials, critical points and bond paths etc…). The computed properties can afterward be displayed in MoProViewer. Then, MoProViewer can be seen as a graphical interface for the VMoPro program.
Furthermore, MoProViewer can be used as a standard molecular viewer, allowing to display a crystal structure (including packing etc…) and to compute standard stereo-chemical properties, as inter-atomic distances, angles, torsion angles but also the so called rigid bond values based on anisotropic thermal motion modelling in the same way you can ask for the distance between two atoms. Of course, you can display thermal motion ellipsoids for any atoms in the model.
MoProViewer can load directly MoPro and PDB molecular files, and XPLOR and CUBE files for properties. It also has an importation tool, allowing you to load CIF, MOLLY and POSCAR files through the Import2MoPro program, which is also part of the MoPro suite.
For properties analysis, MoProViewer can show iso-surfaces of 3D scalar fields stored in XPLOR or CUBE formats, either by loading them from a file, or after a computation done with VMoPro. Once a 3D field has been loaded, you can display it, in 3D, using any isolevel, or you can explore it through a movable slant plane showing any section of the field. You can also compute and display the gradient field of the 3D property that has been loaded.
MoProViewer can also display critical points and/or bond paths obtained after a VMoPro topological analysis, atomic local axis system needed for multipolar refinement, symmetry related molecules (and generate them as long as the crystal symmetry operations are known).

MoProViewer is written in C++, on the basis of the Qt 4.8 (5.1 soon) library, and using libQGLViewer and Armadillo libraries for respectively openGL and linear algebra handling. Credits for the program can be seen using the "About" entry of the "Help" main menu.

In MoProViewer, most of the tools appear in dialog windows that can be set as floating windows, or docked within the main window. This Qt capability (named QDockWidgets) allows the user to configure totally the program layout. Furthermore, user's choices are saved and restored when the program is restarted.



Program overview

MoProViewer main window looks like this :

Main Window

- On the left side is the object tree, representing the loaded molecules and the fragments and atoms it contains.
- Below the window with the loaded molecule is the console log which gives informations about what is being done.
- The status bar at the bottom of the main window shows the current working directory
- On the top of the main window is the menu bar, and below the menu bar the main, symmetry and MoPro toolbars.

Molecules and 3D scalar fields (i.e. maps) can be opened from the Main Menu , then "File" entry. MoPro, PDB, xyz files can be opened directly, while many other formats can be imported using the "Import" option (XD, RES, MOLLY, CIF ...), which needs the "Import2MoPro" program to work properly. Furthermore, CUBE and XPLOR formats for scalar fields are also recognized. In case of CUBE file, which contains both atoms and 3D grid, the program will ask the user if the atoms, the scalar fields, or both, must be loaded from the selected file.



Mouse Usage

Once a molecule has been opened, the mouse commands are the following :

When the focus is on the objects tree window:
Left mouse button click on an atom, molecule  = select atom, and add it to the selection

When the focus is on the viewer window (where the molecule is displayed) :
-
Right mouse button click = open the main contextual menu
- Left mouse button (hold) + move mouse = rotates molecule
- Left mouse button click on the background = unselect all atoms
Middle mouse button (hold) + move mouse = translate molecule
- Middle mouse button click on any drawn object = center view on object
- Left mouse button click on an atom = add atom to the selection
- 
Left_Ctrl + Left mouse button click on an atom = deselect atom, and remove it from the selection
-
Left_Shift + hold left mouse button + move mouse = add atoms to the selection using selection rectangle
Left_Ctrl + hold left mouse button + move mouse =remove atoms from the selection using selection rectangle
- Mouse Wheel = zoom in or zoom out
- L
eft_Ctrl (hold) + mouse Wheel = modify fog depth
- Left_Shift (hold) + mouse Wheel = modify near clipping plane distance

The following apply only when a 3D scalar field slice is active and its dialog window visible :
- Left_Alt + hold Left mouse button + move mouse = rotates around map slice plane center
- Left_Alt + hold Middle mouse button + move mouse = translates map slice plane center along Z axis
- Left_Alt + hold Right mouse button + move mouse = translates map slice plane in XY plane

The following apply only when the "Atom Move Mode" is active :
- Arrow keys = translates moved atom in the XY plane



Opening Files

Files of various formats can be opened by MoProViewer with the File main menu entry as shown below:


MoProViewer opens directly atomic coordinates in PDB, XYZ, POSCAR and atomic coordinates plus electron density parameters in MoPro format. If the location of the Import2MoPro.exe binary file is given in the general preferences dialog, then other formats can be imported using the Import2MoPro tool :


- It is also possible to export atomic coordinates file in the MoPro format using the "Save MoPro file" option. This saves a MoPro parameter file either of the initial molecule (with possible modifications such as axis systems), or of a selection of atoms (in this case missing atoms that are required for axis definitions will be replaced by dummy atoms), or of several symmetry equivalent molecules.
- MoProViewer reads also 3D scalar fields in Xplor or CUBE format. In the CUBE format case, the user is asked to choose wether the program shall read the coordinates part of the file (replacing the current molecule, if any), the scalar field part, or both of them. A loaded scalar field is subsequently stored in the Map Manager tool.

- The "Load critical points" entry allows to read a critical point file generated by VMoPro (cp.dat). Loaded critical points are afterward listed in the Object Tree.
- MoProViewer can also load and save session files (.mpv files) using the "Load session" and "Save session" entries, respectively. A session files keeps the loaded molecules, display styles, critical points and scalar fields.
- Screenshots in various formats (png, jpg...) of what is being shown on the viewer window can be saved with the "Save image" option. A dialog window pops in this case asking informations about the image, such as size and oversampling. An oversampling of 3 is recommended to get high dpi image and a good resolution.
- The "Unload Molecule" option will delete the current molecule, any loaded scalar fields and will also reset all tools.

Notes :
Depending on the type of files loaded, some tools will not be available. For instance there is no possibility to compute electron density map from a PDB file format. Furthermore, the Map Slice tool will stay disabled until a scalar field is loaded.



Current bugs and limitations

- MoProViewer can open an visualize one molecule at a time.
- When a tool is opened and is floating, the windows size is overestimated. The windows size can however been reduced manually if needed.
- Tranparency rendering is not perfect yet, and transparent surfaces can show some artifacts in some orientations.
-Some CUBE files with oblique settings can show some strange shift between molecule and 3D surfaces