ReferenceGuide.Menu History

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March 17, 2009, at 05:51 PM by 148.187.130.153 -
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(:title Menu:)

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March 10, 2009, at 09:38 AM by 148.187.130.153 -
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(:title Menu:)

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March 10, 2009, at 09:36 AM by 148.187.130.153 -
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Menu

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(:title Menu:)

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March 09, 2009, at 05:53 PM by 148.187.130.153 -
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Menu

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Menu

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February 20, 2008, at 05:35 PM by 148.187.130.131 -
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Molecule - Open Molecule Display Settings dialog. Use this dialog to change the atom, bond and residue rendering style and to hide/show the dipole moment (if present).

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Molecule - Open the Molecule Display Settings dialog. Use this dialog to change the atom, bond and residue rendering style and to hide/show the dipole moment (if present).

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February 13, 2008, at 04:43 PM by 148.187.130.131 -
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Analysis menu items are enabled only when a molecule is selected.

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Analysis menu items are enabled only when a molecule is selected.

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Radiation Spectrum - Display infra-red or Raman activity spectrum.

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February 13, 2008, at 04:31 PM by 148.187.130.131 -
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  • change the Occlusion ratio parameter to increase rendering speed or eliminate rendering artifacts: 0 = best quality, 1 = max speed
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  • change the Occlusion ratio parameter to increase rendering speed or eliminate rendering artifacts: 0 = best quality, 1 = max speed
  • Anti Aliasing: increase the number of samples for better looking pictures with little or no jaggies(i.e. steps in diagonal lines or edges); note that each sample is a complete redraw, so rendering time will increase linearly with the number of samples
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February 13, 2008, at 04:24 PM by 148.187.130.131 -
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3D View Properties - Change 3D View properties (width and height only at this time).

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3D View Properties

http://bioinformatics.org/molekel/uploads/ReferenceGuide/3d_view_properties.png

Change 3D View properties.

  • 3D View Size: changes the 3d view size.
  • Depth peeling: these parameters affect the rendering of transparent surfaces:
    • when rendering multiple transparent surfaces increase the Max peels parameter until you can see all the overlapping transparent surfaces
    • change the Occlusion ratio parameter to increase rendering speed or eliminate rendering artifacts: 0 = best quality, 1 = max speed
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July 19, 2007, at 03:27 PM by 148.187.130.131 -
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Event Recorder - Opens the event recording window which allows to save GUI events to a file - Used for testing purpose only.

Event Player - Opens the event player window which allows playback GUI events read from file - Used for testing purpose only.

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July 19, 2007, at 03:24 PM by 148.187.130.131 -
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3D View Properties - Change 3D View properties (width and height only at this time).

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Show/Hide Bounding Boxes - Show/Hide selection boxes.

Shaders - Open Shaders dialog; enabled only if a molecule is selected and the system supports OpenGL 2.0 shaders.

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July 19, 2007, at 03:19 PM by 148.187.130.131 -
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Save Image - Take snapshot of 3D view and save to TIFF file.

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Save Image - Take snapshot of 3D view and save to TIFF or PNG file.

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February 02, 2007, at 11:26 AM by Ugo Varetto -
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Documentation - Open a local copy of Molekel documentation.

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Documentation - Open on-line copy of Molekel documentation. Opens local copy in Molekel < 5.1.

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February 02, 2007, at 09:53 AM by Ugo Varetto -
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Delete Molecule - Delete selected molecule. Does not ask for confirmation.

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Delete Molecule - Delete selected molecule. Asks for confirmation.

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January 03, 2007, at 03:18 PM by Ugo Varetto -
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  • For best results when exporting molecules with atoms rendered as spheres select Display->Molecule->Atom->gluSphere.
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  • For best results when exporting molecules with atoms rendered as spheres select Display->Molecule->Atom->gluSphere.
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  • For best results when exporting molecules with atoms rendered as spheres select Display->Molecule->Atom->gluSphere.
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  • For best results when exporting molecules with atoms rendered as spheres select Display->Molecule->Atom->gluSphere.
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January 03, 2007, at 03:17 PM by Ugo Varetto -
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  • When saving to PostScript a ps extension is automatically added to the file.
  • For best results when exporting molecules with atoms rendered as spheres select Display->Molecule->Atom->gluSphere.
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  • When saving to PDF a pdf extension is automatically added to the file.
  • For best results when exporting molecules with atoms rendered as spheres select Display->Molecule->Atom->gluSphere.
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December 22, 2006, at 04:25 PM by Ugo Varetto -
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Open - Read molecule from file: after the "Open File" dialog opens make sure you select the proper format before selecting the file to open. If you use the "All files - *.*" filter the program will try to guess the file format, which is not usually what you want except for pdb, xyz and other well known file formats. For a list of supported file formats have a loot at the file formats section.

to:

Open - Read molecule from file: after the "Open File" dialog opens make sure you select the proper format before selecting the file to open. If you use the "All files - *.*" filter the program will try to guess the file format, which is not usually what you want except for pdb, xyz and other well known file formats. For a list of supported file formats have a look at the file formats section.

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December 21, 2006, at 11:13 AM by Ugo Varetto -
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Update in progress

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December 21, 2006, at 10:48 AM by Ugo Varetto -
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Per-Molecule Settings - Open Molecule Animation Settings dialog to change animation settings for the selected molecule, see animation settings section? for details.

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Per-Molecule Settings - Open Molecule Animation Settings dialog to change animation settings for the selected molecule, see animation settings section for details.

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December 21, 2006, at 10:45 AM by Ugo Varetto -
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Show/Hide Plane Probe - Show/Hide plane probe: when the plane is visible the menu item is set to "Hide", to "Show" otherwise. The plane probe can be used to visualize a scalar field (e.g. electrostatic potential) and to display the value of the field at a specific point in space by moving the crossair cursor on the plane.

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Show/Hide Plane Probe - Show/Hide plane probe: when the plane is visible the menu item is set to "Hide", to "Show" otherwise. The plane probe can be used to visualize a scalar field (e.g. Electrostatic Potential) and to display the value of the field at a specific point in space by moving the crosshair cursor on the plane.

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  • Move plane: middle mouse button (left on Mac OS)
  • Move cursor on plane left mouse button (currently disabled on Mac OS)
  • Change window and center point used for color mapping: right mouse button
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  • Move plane: middle mouse button (left on Mac OS)
  • Move cursor on plane: left mouse button (currently disabled on Mac OS)
  • Change window and center point used for color mapping: right mouse button
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Show/Hide MEP Scalar Bar - Show/Hide color bar associated with electrostatic potential; use this feature only after a Molecular Electrostatic Potential has been computed and mapped on a surface.

Show/Hide Probe Scalar Bar - Show/Hide color bar associated with Plane Probe; use this feature only after the data to visualize have been generated through the Analysis-Plane Probe dialog.

to:

Show/Hide MEP Scalar Bar - Show/Hide color bar associated with Electrostatic Potential; use this feature only after a Molecular Electrostatic Potential has been computed and mapped on a surface.

Show/Hide Probe Scalar Bar - Show/Hide color bar associated with Plane Probe; use this feature only after the data to visualize have been generated through the Analysis-Plane Probe dialog.

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Used to connect mouse events to camera or selected molecule.

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Used to dispatch mouse events to camera or selected molecule.

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Start/Stop Animation - Start/Stop animation.

Next - Advance to next frame.

Previous - Move to previous frame.

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Start/Stop Animation - Start/Stop animation: starts/stops the animation timer; animation advances to next frame each time the animation timer fires.

Next - Advance to next frame. Disable if animation timer started.

Previous - Move to previous frame. Disabled if animaiton timer started.

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Per-Molecule Settings - Open Molecule Animation Settings dialog to change animation settings for the selected molecule, see animation settings? for details.

Export Animation - Export animation to individual frames or AVI (Windows only). By default all the visible object are animated and exported including any surface generated for molecules which contain vibration/trajectory information.

to:

Per-Molecule Settings - Open Molecule Animation Settings dialog to change animation settings for the selected molecule, see animation settings section? for details.

Export Animation - Export animation to individual frames or AVI (Windows only). By default all the visible objects are animated and exported, including any visible surface.

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  1. click on Analysis-Distance: the distance between the two selected atom will be displayed in the status bar
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  1. click on Analysis-Distance: the distance between the two selected atom will be displayed in the status bar
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  1. click on Analysis-Dihedral Angle: the dihedral angle be displayed in the status bar
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  1. click on Analysis-Dihedral Angle: the dihedral angle be displayed in the status bar
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Note 1: Each time an atom is added to the selection list the Added to selection message appears in the status bar

Note 2: Following the instructions above works fine but the first atom added to the selection list is not highlighted; to highlight the first atom too select the molecule first and then start adding atoms into the selection list

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December 20, 2006, at 11:09 AM by Ugo Varetto -
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Surfaces menu items are enabled only when a molecule is selected.

It is possible to color-code the generated surfaces with molecular electrostatic potential values if the information is available.

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Distance - Compute distance between two atoms

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Distance - Compute distance between two atoms, enabled when two atoms are selected.

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Angle - Compute angle among three atoms

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Angle - Compute angle among three atoms, enabled when three atoms are selected.

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Dihedral Angle - Compute dihedral angle

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Dihedral Angle - Compute dihedral angle, enabled when four atoms are selected.

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Analysis menu items are enabled only when a molecule is selected.

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December 20, 2006, at 11:01 AM by Ugo Varetto -
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Angle - Compute angle between three atoms

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Angle - Compute angle among three atoms

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  1. click on Analysis-Angle: the distance between the two selected atom will be displayed in the status bar

Dihedral Angle - Compute angle between three atoms

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  1. click on Analysis-Angle: the angle among the three selected atom will be displayed in the status bar

Dihedral Angle - Compute dihedral angle

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  1. click on Analysis-Dihedral Angle: the distance between the two selected atom will be displayed in the status bar
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  1. click on Analysis-Dihedral Angle: the dihedral angle be displayed in the status bar
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Documentation - Open a local copy of Molekel documentation.

Molekel Web Page - Open Molekel website url in external browser.

License - Display license and copyright information.

About - Display version and copyright information.

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December 20, 2006, at 10:44 AM by Ugo Varetto -
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Solvent Excluded Surface - Generate SES (Connolly) surface using an internal algorithm (points only) or M.F. Sanner MSMS program (highly recommended, very fast); you can get here

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Solvent Excluded Surface - Generate SES (Connolly) surface using an internal algorithm (points only) or M.F. Sanner MSMS program (highly recommended, very fast); you can get it here.

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Plane Probe - Open the Plane Probe dialog used to generate the data that will be visualized on the surface of the plane probe. Distance - Compute distance between two atoms

  1. unselect all (Ctrl/Command - U)
  2. select two atoms while holding the Shift key down to enable multiple selection
  3. click on Analysis-Distance: the distance between the two selected atom will be displayed in the status bar

Angle - Compute angle between three atoms

  1. unselect all (Ctrl/Command - U)
  2. select three atoms while holding the Shift key down to enable multiple selection
  3. click on Analysis-Angle: the distance between the two selected atom will be displayed in the status bar

Dihedral Angle - Compute angle between three atoms

  1. unselect all (Ctrl/Command - U)
  2. select four atoms while holding the Shift key down to enable multiple selection
  3. click on Analysis-Dihedral Angle: the distance between the two selected atom will be displayed in the status bar
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December 20, 2006, at 10:34 AM by Ugo Varetto -
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Camera - Move/Rotate camera

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Camera - Move/Rotate camera.

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Start/Stop Animation - Start/Stop animation.

Next - Advance to next frame.

Previous - Move to previous frame.

Timestep - Change animation time step.

Per-Molecule Settings - Open Molecule Animation Settings dialog to change animation settings for the selected molecule, see animation settings? for details.

Export Animation - Export animation to individual frames or AVI (Windows only). By default all the visible object are animated and exported including any surface generated for molecules which contain vibration/trajectory information.

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Electron Density - Generate surface(s) from electron density data: molecular orbitals or density matrix.

Grid Data - Generate surface from data read from Gaussian cube files.

Solvent Accessible Surface - Generate SAS as iso-surface.

Solvent Excluded Surface - Generate SES (Connolly) surface using an internal algorithm (points only) or M.F. Sanner MSMS program (highly recommended, very fast); you can get here

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December 20, 2006, at 09:40 AM by Ugo Varetto -
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Used to connect mouse events to camera or selected molecule.

Camera - Move/Rotate camera

Molecule - Move/Rotate selected molecule. Only enabled when a molecule is selected.

Pick Atom/Bond - Enable/Disable picking of individual atoms/bonds/residues. Only enabled when a molecule is selected and Iteraction-Molecule is checked. Information about the selected object is displayed in the status bar.

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December 19, 2006, at 11:55 PM by Ugo Varetto -
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Open - Read molecule from file: after the "Open File" dialog opens make sure you select the proper format before selecting the file to open. If you use the "All files - *.*" filter the program will try to guess the file format, which is not usually what you want except for pdb, xyz and another well known file formats. For a list of supported file formats have a loot at the file formats section.

to:

Open - Read molecule from file: after the "Open File" dialog opens make sure you select the proper format before selecting the file to open. If you use the "All files - *.*" filter the program will try to guess the file format, which is not usually what you want except for pdb, xyz and other well known file formats. For a list of supported file formats have a loot at the file formats section.

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December 19, 2006, at 11:54 PM by Ugo Varetto -
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Open - Read molecule from file, for a list of supported file formats have a loot at the file formats section.

to:

Open - Read molecule from file: after the "Open File" dialog opens make sure you select the proper format before selecting the file to open. If you use the "All files - *.*" filter the program will try to guess the file format, which is not usually what you want except for pdb, xyz and another well known file formats. For a list of supported file formats have a loot at the file formats section.

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December 19, 2006, at 11:43 PM by Ugo Varetto -
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Emphasized

Interaction

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Interaction

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Animation

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Animation

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Surfaces

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Surfaces

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Analysis

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Analysis

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Help

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Help

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December 19, 2006, at 11:41 PM by Ugo Varetto -
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Molecule - Open Molecule Display Settings dialog. Use this dialog to change the atom, bond and residue rendering style and to hide/show the dipole moment (if present).

Background - Change background color.

Show/Hide Plane Probe - Show/Hide plane probe: when the plane is visible the menu item is set to "Hide", to "Show" otherwise. The plane probe can be used to visualize a scalar field (e.g. electrostatic potential) and to display the value of the field at a specific point in space by moving the crossair cursor on the plane. Plane probe interaction:

  • Move plane: middle mouse button (left on Mac OS)
  • Move cursor on plane left mouse button (currently disabled on Mac OS)
  • Change window and center point used for color mapping: right mouse button
    • Change window: move mouse along Y axis
    • Change center point: move mouse along X axis

Show/Hide MEP Scalar Bar - Show/Hide color bar associated with electrostatic potential; use this feature only after a Molecular Electrostatic Potential has been computed and mapped on a surface.

Show/Hide Probe Scalar Bar - Show/Hide color bar associated with Plane Probe; use this feature only after the data to visualize have been generated through the Analysis-Plane Probe dialog.

Show/Hide Axes - Show/Hide Axes at the bottom right corner of the 3D View.

Emphasized

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December 19, 2006, at 11:24 PM by Ugo Varetto -
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Display

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Edit

http://bioinformatics.org/molekel/uploads/ReferenceGuide/edit_menu.png

Unselect - Unselect all selected objects (atoms, bonds, residues, molecules).

Delete Molecule - Delete selected molecule. Does not ask for confirmation.

Clear - Delete all molecules. Asks for confirmation.

Reset Molecule - Resets selected molecule's position and orientation. Enabled only when a molecule is selected.

Reset Camera - Resets viewpoint.

Display

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December 19, 2006, at 11:16 PM by Ugo Varetto -
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File

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File

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December 19, 2006, at 11:16 PM by Ugo Varetto -
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Open - Read molecule from file, for a list of supported file formats have a loot at the file formats section.

Save - Save selected molecule to file.

Save Image - Take snapshot of 3D view and save to TIFF file.

Save to PostScript - Save content of 3D view to PostScript format; transparent geometry will not be exported correctly.

Save to PDF - Save content of 3D view to PDF format; transparent geometry will not be exported correctly.

to:

Open - Read molecule from file, for a list of supported file formats have a loot at the file formats section.

Save - Save selected molecule to file.

Save Image - Take snapshot of 3D view and save to TIFF file.

Save to PostScript - Save content of 3D view to PostScript format; transparent geometry will not be exported correctly.

Save to PDF - Save content of 3D view to PDF format; transparent geometry will not be exported correctly.

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December 19, 2006, at 11:15 PM by Ugo Varetto -
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  • Open - Read molecule from file, for a list of supported file formats have a loot at the file formats section.
  • Save - Save selected molecule to file.
  • Save Image - Take snapshot of 3D view and save to TIFF file.
  • Save to PostScript - Save content of 3D view to PostScript format; transparent geometry will not be exported correctly.
  • Save to PDF - Save content of 3D view to PDF format; transparent geometry will not be exported correctly.
to:

Open - Read molecule from file, for a list of supported file formats have a loot at the file formats section.

Save - Save selected molecule to file.

Save Image - Take snapshot of 3D view and save to TIFF file.

Save to PostScript - Save content of 3D view to PostScript format; transparent geometry will not be exported correctly.

Save to PDF - Save content of 3D view to PDF format; transparent geometry will not be exported correctly.

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December 19, 2006, at 11:13 PM by Ugo Varetto -
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  • Open - Read molecule from file, for a list of supported file formats have a loot at the file formats section.
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  • Open - Read molecule from file, for a list of supported file formats have a loot at the file formats section.
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December 19, 2006, at 11:12 PM by Ugo Varetto -
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http://bioinformatics.org/molekel/uploads/ReferenceGuide/file_menu.png Open - Read molecule from file, for a list of supported file formats have a loot at the file formats section.

Save - Save selected molecule to file.

Save Image - Take snapshot of 3D view and save to TIFF file.

Save to PostScript - Save content of 3D view to PostScript format; transparent geometry will not be exported correctly.

Save to PDF - Save content of 3D view to PDF format; transparent geometry will not be exported correctly.

to:

http://bioinformatics.org/molekel/uploads/ReferenceGuide/file_menu.png

  • Open - Read molecule from file, for a list of supported file formats have a loot at the file formats section.
  • Save - Save selected molecule to file.
  • Save Image - Take snapshot of 3D view and save to TIFF file.
  • Save to PostScript - Save content of 3D view to PostScript format; transparent geometry will not be exported correctly.
  • Save to PDF - Save content of 3D view to PDF format; transparent geometry will not be exported correctly.
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December 19, 2006, at 11:11 PM by Ugo Varetto -
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Open - Read molecule from file, for a list of supported file formats have a loot at the file formats section.

to:

Open - Read molecule from file, for a list of supported file formats have a loot at the file formats section.

Save - Save selected molecule to file.

Save Image - Take snapshot of 3D view and save to TIFF file.

Save to PostScript - Save content of 3D view to PostScript format; transparent geometry will not be exported correctly.

Save to PDF - Save content of 3D view to PDF format; transparent geometry will not be exported correctly.

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December 19, 2006, at 11:07 PM by Ugo Varetto -
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Open - Read molecule from file, for a list of supported file formats have a loot at the file formats section.

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Open - Read molecule from file, for a list of supported file formats have a loot at the file formats section.

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December 19, 2006, at 11:06 PM by Ugo Varetto -
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  • Open - Read molecule from file, for a list of supported file formats have a loot at the file formats section.
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Open - Read molecule from file, for a list of supported file formats have a loot at the file formats section.

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December 19, 2006, at 11:05 PM by Ugo Varetto -
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http://bioinformatics.org/molekel/uploads/ReferenceGuide/menu.png

  • Open - Read molecule from file, for a list of supported file formats have a loot at the file formats section.
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http://bioinformatics.org/molekel/uploads/ReferenceGuide/menu.png

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http://bioinformatics.org/molekel/uploads/ReferenceGuide/file_menu.png

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http://bioinformatics.org/molekel/uploads/ReferenceGuide/file_menu.png

  • Open - Read molecule from file, for a list of supported file formats have a loot at the file formats section.


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December 19, 2006, at 11:05 PM by Ugo Varetto -
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http://bioinformatics.org/molekel/uploads/ReferenceGuide/menu.png

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http://bioinformatics.org/molekel/uploads/ReferenceGuide/menu.png

  • Open - Read molecule from file, for a list of supported file formats have a loot at the file formats section.
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December 19, 2006, at 11:02 PM by Ugo Varetto -
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http://bioinformatics.org/molekel/uploads/ReferenceGuide/interaction_menu.png

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http://bioinformatics.org/molekel/uploads/ReferenceGuide/interaction_menu.png

Animation

http://bioinformatics.org/molekel/uploads/ReferenceGuide/animation_menu.png

Surfaces

http://bioinformatics.org/molekel/uploads/ReferenceGuide/surfaces_menu.png

Analysis

http://bioinformatics.org/molekel/uploads/ReferenceGuide/analysis_menu.png

Help

http://bioinformatics.org/molekel/uploads/ReferenceGuide/help_menu.png

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December 19, 2006, at 10:59 PM by Ugo Varetto -
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http://bioinformatics.org/molekel/uploads/ReferenceGuide/file_menu.png

Display

http://bioinformatics.org/molekel/uploads/ReferenceGuide/display_menu.png

Interaction

http://bioinformatics.org/molekel/uploads/ReferenceGuide/interaction_menu.png

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December 19, 2006, at 10:57 PM by Ugo Varetto -
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http://bioinformatics.org/molekel/uploads/ReferenceGuide/file_menu.png

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December 19, 2006, at 10:54 PM by Ugo Varetto -
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Update in progress

Menu

http://bioinformatics.org/molekel/uploads/ReferenceGuide/menu.png

File

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