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Preferences |
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[Directories...][Files...] [Plot 2D...][Plot 3D...][Grid plot][Probe Color...]
This menu gives access to a number of commands allowing the User to set up some preferences on ALMOND graphical applications and to define the path for help files and model library directories.
This command shows the following dialog window:
Default model library path
ALMOND can use two different paths for storing models. These were labeled local and global, since many Users would like to have two categories of models:
- Global models. Accessible to many users and stored in shared directories. Contains well tested models with a general-interest use
- Local models. Accessible only to a certain use. Might contain models under development of for particular purposes
This control allows to define which one of these paths is used by the commands which need to access to the model libraries.
Global model library path
The path defined here is used by ALMOND to locate and retrieve global models. It should correspond with a previously existing directory.
By default, the models are stored in the subdirectory models, which hangs from the main ALMOND installation path. Since usually normal users don't have writing permission in this directory, this is a good place to store important models which should be accessed in read only model.
Local model library path
The path defined here is used by ALMOND to locate and retrieve local models. It should correspond with a previously existing directory.
Models generated by the User need to be stored in a directory where the User has full reading and writing permissions.
Help path
This text field is used by ALMOND to locate the on line manual. The user can change the location if necessary.
Help browser
Full path and application name of the HTML browser which will be called by ALMOND in order to access on-line to the help files. The default is mozilla, but other browsers (e.g. netscape) can also be used.
OK
Save options and exit from this menu
Cancel
Exit from this menu without saving
Help
Opens the on line help.
Extension default
The file browsers opened by the series import dialog, present files with a fixed extension. For example, if the User select mol2 as the file format for the series import procedure, ALMOND will search and show all the *.mol2 files. This is convenient when single files are imported, but not when list files with .lst or .list extension are selected often. Select between the File type and .lst options to choose the filter mask more appropriate for your needs.
OK
Save options and exit from this menu
Cancel
Exit from this menu without saving
Help
Opens the on line help.
ALMOND presents data in several different 2D and 3D plots. Every plot is an independent application and the User can always setup the preferences using the plot interface (see plot and plot3D sections). However, this menu allows the User to set-up the default settings for both 2D and 3D plots. These will be written to a local preference file and from this moment, every new 2D or 3D plot will use these settings by default.
2D and 3D plot preferences dialog windows are shown here:
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- Symbol points
- Points, circles, squares, crosses (only for 3D plots), molecule numbers or molecule names can be selected as default in the 2D or 3D plot.
- Symbol size
- Any real value from 0.0 to 4.0 (8.0 for 3D plots) can be selected. 0.5 or 1.0 are good choices.
- Symbol color
- The objects in 2D or 3D plots can be coloured by their Type if the type has been defined in the File>>>Object type menu. Moreover objects can be automatically coloured by Spectrum if one value of the activity is present. Points on the 3D plots can even be coloured by Depth, so that colors from red to blue are given depending on how far they are from the observer.
- Background
- Black or White are the options to select from.
- Symbol font
- Small or Large are the font used to print molecule names and numbers.
- Display structures
- No yet implemented.
- Line smoothing
- With this option the User choose whether to apply line smoothing (antialiasing) to the plots. In SGI platforms we suggest to set it to On.
- Monochrome
- If selected, the plots will be displayed only in black and white
- Pointer step (2D plots only)
- No yet implemented.
- Fog - Grid cage - Perspective (3D plots only)
- This three options will influence the way the 3D plots are drawn on the screen.
Every grid plot is an independent application and the User can always setup the preferences using the plot interface (see the plotGrid manual). However, this menu allows the User to set-up the default settings for grid plots. These will be written to a local preference file and from this moment, every new grid plot will use these settings by default.
Grid plot preferences are distributed in several categories :
- General contains the preferences common to all the grid plots.
- Molecules set the default style, label and color options of molecule structures.
- Raw Fields, Filtered Fields, Contrib. Fields define the default aspect of the MIF of the related grid plot.
Preferences>>>Grid plot>>>General...
Allows to enable/disable some general visualization options:
| stereo | enable/disable stereo hardware. |
| spin | enable/disable spin animation. |
| decoration | enable/disable some extra window decoration. The decoration includes some buttons and thumbwheels for rotating and scaling the scenario. |
| fog | enable/disable fog. When enabled, some fog is added to simulate the depth and objects far from the observer will appear darker. |
| perspective | enable/disable perspective. When perspective is on, objects far from the observer look smaller, when it is off an orthographic perspective is used. Perspective on is useful for small molecules, while can make difficult to visualize large molecules. |
| rock | enable/disable a continuous oscillating rotation of the Y axis. Rocking can be useful to appreciate the third dimension in small molecules but can be very disturbing when visualizing large scenarios, especially in positions far from the rotation center. |
| grid | Toggles on and off the display of a cube representing the extents of the grid cage. |
| clipboard show | the different clipboard models are none, local or global (see plotGrid manual). |
Preferences>>>Grid plot>>>Molecule...
Style
Select the kind of representation of the molecules (see plotGrid manual).
Label
Define the labeling scheme and the font type and size used for the labeling (see plotGrid manual).
Coloring scheme
Select the coloring scheme to apply: palette, by atom type or by property (see plotGrid manual). If the palette option is selected, a palette window will pop up for color selection.
Preferences>>>Grid plot>>>Raw fields...
Preferences>>>Grid plot>>>Filtered fields...
Preferences>>>Grid plot>>>Contrib. fields...
The dialog box is the same for the three field types, only the name of the window changes. As an example, The Raw fields window is shown below.
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 within 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.
show negative field
show positive field
toggles on and off the display of positive or negative data
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.
show planes
In isocontour representations, these controls toggle on and off the display of the contour lines in the X, Y and Z planes.
Each field is associated to one color which can be modified by mean of the probe color dialog box.
Preferences>>>Probe Color...
The color of the probe is important in three situations :
- When raw fields are plotted, the positive part of the field is always yellow, while the color of the negative part of the field is set according to the chooser value.
- When filtered fields are plotted, the color of the field always corresponds to the associated probe color.
- When a correlogram is marked in a profile plot, its color is a blend of the colors of the two probes involved in it, e.g. if Probe 1 is ivory and Probe 2 is red, marked profile of correlogram 12 is orange.