Welcome page and Program overviewTools and toolbarsThe Contextual menu and the Selection The Display settings


 
Most of the tools allowing to configure the computation and the display of electron density derived properties can be found either in the main menu then "Tools" entry, or using the main toolbar :

tools menu


1  -  2D Contour Map Viewer : a dialog allowing to plot 2D contour maps
2  -  Advanced Selection : to perform atom selection using various criteria
3  -  Log Window : the text (read-only) window giving various informations to the user, about what is being done by the program. 
4  -  Object Tree : gives the detail of the molecule (and its generated symmetry equivalent molecules), of its fragments and atoms, and also of the critical points loaded.
5  -  3D Isosurface Map : it allows to configure and to run a computation with VMoPro of 3D scalar field properties such as electron density, electrostatic potential or topological analysis. The map written after such computation can be displayed and managed using the "3D map manager" tool.
6  -  2D contour Map : it allows to configure and to run a computation with VMoPro of 2D contour map of various properties. The grid file containing the contour values written after such computation can be displayed using the "2D Contour Map Viewer".
7  -  Electrostatic Moments Computation : to compute electric dipoles and quadripoles of the molecule or of a selection of atoms in the molecule. Computed moments can be displayed and configured afterward using the "Electrostatic moments manager"
8  -  3D Map Manager : this tab widget allows to configure all 3D maps loaded, either directly from the main menu, or after a computation using the "3D isosurface map" tool.
9  -  3D Map Slice Managerthis tab widget allows to configure all the 2D map slices created to explore a 3D scalar field.
10  -  Summary Tree : a read-only dialog summarizing molecule names, loaded maps and running VMoPro computations.
11  -  3D Map Color Chart : this tool is used to colour a loaded scalar field using any other loaded scalar field's values. It can be used for instance to colour a 0.001 e/A3 electron density map on the basis of the molecular electrostatic potential.
12  -  Atom Properties Editor : to check all properties of an atom 
13  -  Interaction Energy : a dialog window allowing to compute electrostatic interaction energy between two sets of atoms.
14  -  Atom Move : a dialog window allowing to change precisely the position of a given atom.
15  -  Electrostatic moments manager : a tab window used to change the appearance of the computed electrostatic moments. 


The Toolbars


The main toolbar

Some of the tools listed above can also be invoked using the main toolbar :
                                                                                                                                       
tb
                                                14                                                       12     5    6    9   7    13


The other buttons of the toolbar are the following :
tb
     A    B    C    D     E             F    G    H     I     J       K                                                L    M    N

All these actions will ask for clicking on one or more atoms in the viewer (for instance pick two atoms to measure the distance between them). The behaviour of some actions (A, B, C, D, E, F and H) can be changed from the preferences dialog (Main menu, Options then Preferences) so that, for instance, the distance button remains active, or deactivates, between two distances measurement.

The toolbar buttons labelled above are :

A. To measure and show the distance between two atoms
B. To measure and show the valencial angles forming tree atoms
C. To measure and show the torsion angle formed by four atoms
DTo measure and show the Hirschfeld rigid bond test value between two atoms
E. To show the thermal displacement ellipsoid of one atom. The probability can be changed from the display settings "Bonds and atom style" tab.
mkbondF. To create, or delete if already present, a covalent bond between two atoms. This is for representation purposes (image generation), and a created bond will not propagate between symmetry generated molecules
G. To show the definition of one atom local axis system (i.e. which atoms are selected to define a local axis)
H. To change the local atomic axis system of an atom. This will ask to select an atom, then a dialog window pops up asking to select the type of axis system :

axis redefinition 1

After validation two atoms must be clicked to choose the axis definition, then a validation window appears to ask the user to confirm his choice.

axis redefinition 2

I. To show the atom local axis system after orthogonalization.
J. To draw the label of one picked atom
K. To focus the view approx. 10A in front of one picked atom. 
L. To show the valence electron density constrain scheme of one picked atom.
M. To show the multipolar electron density constrain scheme of one picked atom.
N. To show the kappa electron density constrain scheme of one picked atom.



The MoPro  toolbar



This toolbar allow to navigate easily between several MoPro files of the same family (i.e. same prefix). Using this to change parameter file is different than loading a parameter file from the Main Menu. Indeed, using the MoPro toolbar will preserve the configuration of the tools dedicated to properties computations, so that it is easy to plot, for instance, a static deformation electron density map in a given plane for several stages of a multipolar refinement, i.e. for several versions of the MoPro parameter file. 



The Symmetry  toolbar



This toolbar gives access to symmetry equivalent molecules generation, either using the Ortep code of a given symmetry operator, or by clicking on the "Sym. Position" button to show on the viewer, as spheres, the positions of the symmetry equivalent molecules center of masses. Clicking on one sphere will generate the corresponding molecule in the crystal. The red sphere in this case corresponds to the asymmetric unit molecule (as defined in the original file).