plotGrid

plotGrid is the application used by GOLPE to visualize field or chemometrical data together with molecular structures. The application can be also used to export the data to standard formats and to print or save the images in RGB format.

The plotGrid application is usually started from a command in the GOLPE plot>>>Grid plotsubmenu and the field or chemometrical data is automatically set at start-up. On the contrary, the molecular structures should be imported by the User, either using the drag an drop import mechanism described below of the command Molecules>>>Molecules Manager>>>Add.

If the User wants to import many of molecules in different plotGrid instances, he can load these molecules once and then save them as a "template". Then, successive instances of plotGrid will open the same molecules at start-up automatically.

drag and drop import

The simplest and fastest way to import molecules into plotGrid is to use "drag and drop". For using this mechanism, start opening the folder containing the structures using the Indigo Magic Desktop directory view. Click on the Directory icon in your Desktop and navigate for the directory three until you can see the files that you want to import. Select one or more icons (up to 100), drag and drop them on the plotGrid window. plotGrid will read the files and import them one after the other.

By default plotGrid will color the first imported structure "by atom type" and will assign different palette colors to successive structures.

plotGrid recognizes the format of the molecular structure by the extension of the file. If you try to import a file with a wrong extension or without any extension, the import can fail. The following extensions are recognized:

mouse and plotGrid modes

In plotGrid the mouse has different uses depending the application mode:

In pick mode, it is possible to press <Alt> to change to browse mode temporarily, the pick mode will be restored when the key was released. This allows to rotate or translate the molecule without actually exiting from the pick mode.

plotGrid menu

[File][View][Data][Molecules]

File>>>Save

plotGrid can save the field or chemometrical data in Insight (.grd) or SYBYL (.cnt) formats. Please refer to the respective manual of these applications for details about how to import.

plotGrid can also save the scenario in Inventor (.iv) 2.0 format. Inventor files can be imported in SceneViewer and showcase as interactive 3D objects, can be exported to rendering programs, used in inperson remote conferences, etc...

. When exporting molecular structures in Inventor format we recomend to avoid the use of wireframe style. This can lead to some problems when importing in showcase.

The user is asked to provide a name for the output file using a standard file dialog.

plotGrid can send the contents of the screen directly to a printer or write a file either in PostScript or RGB format.

The User can define output options in a dialog like this. Since it is a context sensitive dialog not all available options are shown in the picture below.

plotGrid always tries to produce a high contrast image and would ignore fog and background settings. If you want to obtain a exact representation of the image as it is on the screen, please use the snapshot utility instead.

Use this command to quit the application.

Toggle this control to change between view mode and pick mode. The different mouse modes were described above.

The position of the virtual camera and the scale is stored in an internal clipboard, common for all applications in the Desktop. Select View>>Paste view in the same or in a different plotGrid application to restore this point of view.

This option is very useful to show exactly the same point of view in different plotGrid applications representing different data.

The view can be copied and pasted only between applications using the same type of cameras. If one of the plotGrids is using perspective and the other no, the copy and paste will not work.

The position of the virtual camera and the scale, stored in the internal clipboard using View>>>Copy view, are applied to the current scenario.

This option is very useful to show exactly the same point of view in different plotGrid applications representing different data.

The view can be copied and pasted only between applications using the same type of cameras. If one of the plotGrids is using perspective and the other no, the copy and paste will not work.

Restores the original point of view and scale, the same that was shown when the application was open.

Applies a camera position and an scale that allows to visualize the entire content of the scenario.

View>>>Preferences

Opens a dialog where the User can select some general preferences of the application.

General

Allows to enable/disable some general visualization options:

Clipping planes

The scenario has two clipping planes, one nearer to the observer and other at the far end. Only objects between these two clipping planes are shown.

When the option auto is enabled, the application changes dynamically these values to accommodate all the elements in the scenario. If the option auto is toggled off, the User can change the positions of the far and near clipping plane to remove some parts far from the observer or near to the observer.

Labels

When the mouse picking mode is active, the atoms selected are labeled using a string containing:

1. The name of the molecule. The name of the file, including the extension.
2. The name of the atom. One or two characters in uppercase plus the sequential atom number.
3. The name of the residue. Only applicable to PDB files, three characters identifying the type of the residue and other three identifying their number.

Using these controls the presentation of there three parts can be customized to include only the information required.

Changes are applied to the scenario immediately. To exit from the dialog press Quit. To restore the default values press the Default button.

This menu contains options relative to the presentation of the field or chemometric data imported from GOLPE.

plotGrid represents only the grid nodes that have values over a certain cutoff. The application allows the User to define two separated cutoff's: one for positive and one for negative values.

By default, positive values are represented as yellow symbols/contours/surfaces, while negative values are represented as cyan symbols/contours/surfaces. In this dialog it is also possible to change the color and other visual properties of the elements representing positive or negative data.

Negative values:

Positive values:

The control show toggles on and off the display of positive or negative data

The scales define the positive and negative cutoff values. When the data is represented as contours or surfaces, these values are actually isocontour values:

• For positive values, the surface or contour will enclose all the field nodes with values lower than the positive cutoff.
• For negative values, the surface or contour will enclose all the field nodes with values higher than the negative cutoff.

When the data is represented as symbols, these cutoff define a limit for showing or not a certain grid node.

By default, the positive and negative cutoff are set to 1/3 of the positive maximum and negative minimum, respectively. To change the levels simply drag the scale, the changes will be reflected in the graphics as soon as you release the mouse button.

Symbols, contours and surface are represented in the scenario using a colored material: yellow for the positive values and cyan for the negative. The User can change the visual properties of this material pressing the material button. The button shows a dialog like this:

The User can edit the color of the material with respect to the Ambient light (Amb:) Diffuse light (Diff:), Specular light (Spec:) and Emissive light (Emis:). Apart from the color, the dialog allows to change the shininess and the transparency of the material.

With respect to the transparency we must warn the User that, even if transparent surfaces are very nice and helpful sometimes, the use of transparency slows down the rendering of the graphics quite a lot. Mainly if they are applied to symbols like spheres or cubes.

All these properties modify the aspect of the surfaces and some of the objects (spheres, cubes and points). For contours and crosses, only the diffuse color has some effect.

The changes are applied immediately, to close this dialog press the Quit button. To restore the default setting press theDefaults button.

This command shows the following dialog:

show data as...

Allows the User to change the representation of the data between surface, contours and symbols. Surface and contours are basically isocontour representations. In the symbols representation mode, each grid node whitin the range defined by the positive and negative cutoff will be represented by a symbol (a cross, a point a cube or a sphere) of a size proportional to the absolute value represented. For example: a sphere representing a value of 0.03 will be bigger than a sphere representing a value of 0.02. The points are an exception and are represented using the same size independently of the grid node value.

type

Define the type of symbol to use: points, crosses, spheres and cubes. The faster representation is obtained with crosses, but spheres and cubes can produce nice and clean representations in some cases. As a general rule, do not try to use symbol representations for very large fields (more than 100.000 grid nodes) because the rendering of the plot can be very slow. In these case use surfaces or contours.

size

Define the base size used for the symbols, in arbitrary units.

grid

Toggles on and off the display of a cube representing the extents of the grid cage.

clipboard

Toggles on and off the use of the clipboard. When it is on, plotGrid will highlight the variables selected by the User in 2D plots of variables. When it is off, the program will be insensitive to the selection of the User. Please see the plot intercomunication section for further info.

show planes

In isocontour representations, these controls toggle on and off the display of the contour lines in the X, Y and Z planes.

The changes are applied immediately, to close this dialog press the Quit button. To restore the default setting press theDefaults button.

Data>>>Symbols

Data>>>Contour

Data>>>Surface

These menu options allow the User to change the representation of the data between surface, contours and symbols. Is a shortcut to the command Data>>>Data options>>>show data as...

Data>>>Clipboard

Toggles on and off the use of the clipboard. When it is on, plotGrid will highlight the variables selected by the User in 2D plots of variables. When it is off, the program will be insensitive to the selection of the User. Please see the plot intercomunication section for further info.

Data>>>Grid

Toggles on and off the display of a cube representing the extents of the grid cage.

This menu contains commands related to the import of molecular structures and the edition of their aspect.

plotGrid can import up to 100 molecules. The Molecules Manager is a plotGrid utility which allows the User to:

1. visualize the list of the molecules imported,
2. add, remove and hide molecules
3. edit the color and stile of each one independently.

The scrolled list shows a line for each molecule imported, where it is written the name of the file (including the extension) and a label indicating the color scheme.

Add

Press this button to add new molecules. The use of this button is an alternative to the drag and drop import mechanism described above with the inconvenient that this button is used to add molecules one by one.

The button will present a standard file selection dialog where the User can select the file to import. plotGrid recognize the format of the molecular structure by the extension of the file. If you try to import a file with a wrong extension or without any extension, the import can fail. The following extensions are recognized:

The first molecule imported will be colored by atom type. Sucesive molecules will be colored of different palette colors.

Remove

Select one molecule from the list and press this button to remove the corresponding molecule from the scenario.

Molecules Color

Select one molecule from the list and press this button to edit its color. The Molecules Color dialog is described in detail in Molecules>>>Molecules Color

Molecules Style

Select one molecule from the list and press this button to edit its style. The Molecules Style dialog is described in detail in Molecules>>>Molecules Style

Hide

Select one molecule from the list and press this button to toggle on and off its hidden status. Hidden molecules are present in the list but not shown in the scenario until their hidden status is toggled on.

The molecules already imported in the scenario can be saved as a template for the currently active GOLPE dataset. pressing the button Save As Template. Once a template is saved, any new plotGrid launched by GOLPE will load all these molecules at start-up. The button Defaults will restore the start-up status. If no template was present it will simple remove all molecules. If there was a template it will restore it. Press the Quit button to close the dialog.

In plotGrid, the molecules can be colored using three different coloring schemes:

Selections made using this command directly from the menu will be applied to every molecule present in the scenario. If you want to select the color of only one molecule call this command using the Molecules Manager

The command opens the following dialog:

Coloring scheme

Select the coloring scheme to apply: palette, by atom type or by property, as describe above.

Palette

The buttons are selectable only when the coloring scheme selected is palette. Click on any button to apply this color.

Selections made using this command directly from the menu will be applied to every molecule present in the scenario. If you want to select the color of only one molecule call this command using the Molecules Manager

The command opens the following dialog:

Wireframe

Sticks

Ball&Sticks

CPK

Select the kind of representation used for the molecule/s. Wireframe is fast and usually a good choice for large molecules. Sticks and ball and sticks is preferable for small molecules. CPK representation allows to appreciate the volume of the molecules.

Show hydrogens

Toggles on and off the representation of any hydrogen atoms in the molecules.

No labels

Atom labels

Residue labels

Defines the labeling scheme. By default no labels are shown. The User can select if add labels the atoms, or the residues. This last option is only available for PDB molecules. Residue labels are applied near to the alpha Carbon.

Labels are rendered in the scenario using the font and size specified in this dialog. The default is Helvetica font and 10 points size.

Wireframe

The Width scale changes the width of the line used to represent the molecule

Balls

The Complexity scale changes the quality of the representation of spheres (in Sticks, Ball and Stick, and CPK representations). Selecting a higher value produces nicer structures but the rendering will be slower.

The Radius scale changes the radius of the spheres (in Ball and Stick, and CPK representations).

Sticks

The Round cap toggles the capping stile of the sticks. When it is selected, the sticks will have a rounded end. Capped sticks are nicer but the rendering will be slower.

The Complexity scale changes the quality of the representation of sticks (in Sticks and Ball and Stick representations). Selecting a higher value produces nicer structures but the rendering will be slower.

The Radius scale changes the radius of the sticks (in Sticks and Ball and Stick representations).

Molecules>>>Wireframe

Molecules>>>Sticks

Molecules>>>Ball and stick

Molecules>>>CPK

All these commands are shortcuts to Molecules>>Molecules Style>>>Wireframe/Sticks/Ball&Sticks/CPK. Please notice that selections made using these commands will be applied to all the molecules in the scenario. To modify the Style of only one molecule use Molecules>>>Molecules Manager instead.

stand-alone mode use of plotGrid

plotGrid can be used as a stand-alone tool for visualizing molecules, typing:

plotGrid filename

where filename is a molecule structure in format .mol2, .pdb, .car or .kout. If the GOLPE installation directory is not set in the PATH environment variable, the command should be preceded by the full path (i.e. /usr/local/golpe/plotGrid).

When used in stand-alone mode, the default coloring scheme is "by property".