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Chapter 16. Menu Preferences (Alt-S)
This menu gives access to options that user can define to select preferences on graphical applications, help files location or model library paths.
16.1. Preferences->Directories
By clicking on this button the following window will appear:
- Default model library path
The User can choice two kind of library model to use according to the path in the "Global model library path" and "Local model library path" fields:
select Global to use the VolSurf library models inclused in the VolSurf package.
select Local to use the new library models created by the User.
- Global model library path:
This text field is used by VolSurf to locate and retrieve the models present in the VolSurf package. By default the models are stored in the models subdirectory in the VolSurf installation path.
Note: Since usually normal users haven't the necessary permissions to write in the VolSurf installation directory, it is always advisable to copy the VolSurf library models in a subdirectory of the User's home (i.e. /home/stan/volsurf) to modify them, and then set the Global model library path accordingly.
- Local model library path:
This text field is used by VolSurf to locate and retrieve the VolSurf models that the User will create. By default the models are stored in the models subdirectory in the the User's home directory. The User can modify this path in order to select the proper model library directory. From that moment VolSurf will store the library models in this new defined directory.
- Help path:
This text field is used by Volsurf to locate the on line manual. The user can change the location if necessary.
Press OK to save options and exit from this menu or press Cancel to exit from this menu without saving; the Help button opens the on line help.
16.2. Preferences->Files
- Extension default
During the molecules import phase VolSurf by default is looking for files with a fixed extension. For example, if the User select mol2 as the file format for the series import procedure, VolSurf will search and show all the *.mol2 files. Select File type here to allow this filtering scheme. Conversely, if the User choose the .lst option VolSurf will filter and show only the list files (*.lst).
- Delete .pdb files
Select No (as default) to save the .pdb files or Yes to remove the .pdb and .aamd files after the VolSurf computation.
- Delete .kout files
Select No (as default) to save the .kout files or Yes to remove the .kout files after the VolSurf computation.
Note: For mol2 file import, if "run GRID & VolSurf" is selected in the File->Import->Series... dialog, the .aamd, .pdb and .kout files are saved in the .vol.Files directory; instead, if "run GRIN only" is selected the .aamd, .pdb and .kout files cannot be removed and they are saved in the directory where the User have run the VolSurf programme.
Warning When importing .kout files the .aamd and .pdb files are necessary to compute some VolSurf descriptors like the "Best Volumes" and "Polarizability; otherwise the -99 value is assigned to these descriptors."
Press OK to save options and exit from this menu or press Cancel to exit from this menu without saving; the Help button opens the on line help.
16.3. Plot configuration
The following plots are available:
Preferences->Plot 2D
Preferences->Plot 3D
Volsurf uses many different graphics representations of the data. This menus give access to to commands that can be selected once by the User as preferences and then saved in the preference file. Then, VolSurf will always start the graphic application with the parameters set in this sections.
2D and 3D plot preferences windows are represented here:
- Symbol
points, circles, squares, crosses (only for 3D plots), number for molecule numbers or name for 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 can be a good choice.
- 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 colours 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 font or Large font are the options for the font used to visualize and print molecule names and numbers.
- Display structures (only for 2D plot)
when this option is selected each time the User will open a PCA or PLS score plot, the PlotGrid window appears to display the 3D molecular structure of the objects reported in the plot. To display the structure the User simply has to click on the object.
- Line smoothing
with this option the User choose whether to apply smoothing (i.e. anti alias) to the plots. We suggest to select it.
- Monochrome
if selected, the plots will be displayed only in black and white.
- Pointer step (only for 2D plots)
with this option the User can select the sensitivity (i.e. the step) for the movement of the cursor when driven by the keyboard.
- Fog - Grid cage - Perspective (only for 3D plots)
this three options will influence the way the 3D plots are drawn on the screen, so it is up to the User's personal "taste" which ones to activate.
Press OK to save options and exit from this menu or press Cancel to exit from this menu without saving; the Help button opens the on line help.
16.4. Preferences->Miscellaneus
- Default calculation definition
Selecting No the Calculation Parameters window appears when the User imports fields (see also File->Import->Fields...) or uses the the Calculation->Recompute command.
- Help Browser path:
This is the path for the browser programme to visualize the html manual with the Help->help browser command.
- Charge computation method
The calculation of the atomic charges for the HETATMs can be made with the standard Saunderson algorithm method of GRIN by selecting Std. or it can be made with the semiempirical AM1 method by selecting AM1.
Press OK to save options and exit from this menu or press Cancel to exit from this menu without saving; the Help button opens the on line help.
16.5. Preferences->Grid Plot
With this menu is possible to set as default various visualization options for the PlotGrid external application.
16.5.1. Preferences->Grid Plot->General
this dialog is the same of that opened with the View->Preferences command in the plotGrid application.
16.5.2. Preferences->Grid Plot->Molecules
These options can be used to change the default visualization properties of the molecules visualized in the PlotGrid application. This dialog is like to that:
- Style
Select the kind of representation used for the molecule/s. Wireframe is fast and usually a good choice for large molecules. Sticks and Ball&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.
- Label
Defines the labeling scheme. By default no labels (No Labels)are shown. The User can select if add labels the atoms (Atom Labels), or the residues (Residue Labels). 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 under in the two options. The default is Courier font and 8 points size.
- Coloring scheme
Select the coloring scheme to apply: palette, by atom type or by property. for more details about the molecules color see the Molecules->Molecules Color in the external PlotGrid application.
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