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Using the Drop-Down Menus All of BioLuminate's functionality can be accessed via the drop-down menus. Buttons can be added and removed to any toolbar by right-clicking on a toolbar and selecting Customize. Using the toggle Table includes a number of shortcut buttons atop a list of entries (rows) currently in the BioLuminate Workspace.
Using the Drop-Down Menus All of BioLuminate's functionality can be accessed via the drop-down menus. Buttons can be added and removed to any toolbar by right-clicking on a toolbar and selecting Customize. Using the toggle Table includes a number of shortcut buttons atop a list of entries (rows) currently in the BioLuminate Workspace.
Using the Drop-Down Menus All of BioLuminate's functionality can be accessed via the drop-down menus. Buttons can be added and removed to any toolbar by right-clicking on a toolbar and selecting Customize. Using the toggle Table includes a number of shortcut buttons atop a list of entries (rows) currently in the BioLuminate Workspace.
accessed via the drop-down menus. File - For import/export and fle saving Edit - For selecting and editing structures in the Workspace Style - For applying molecular styles to the Workspace contents View - For adjusting global Workspace display settings Tools - For performing various analyses, and accessing superposition and alignment tools Tasks - For running calculations
Window - For raising and closing application windows Help - Links to various Help resources Using the Toolbars Show and hide the toolbars: Click on the respective toolbar title to toggle that toolbar between being shown and being hidden. For example, toggle on the Project toolbar, and click the button to bring up the Project Table. Buttons can be added and removed to any toolbar by right-clicking on a toolbar and selecting Customize. BioLuminate 2014 User Interface Mouse Controls Rotate xy: Left button
Rotate z: Shift+middle and right buttons
Translate: Click and hold the middle button while moving the mouse
Select Multiple Atoms: Shift+left button
Zoom: Hold the right button while moving the mouse Customize Mouse Buttons: Edit > Settings > Mouse Actions, from this menu the mouse buttons can be customized for PyMOL, 2-button, 3-button, and track pad mouse confgurations. Display right-click contextual menus: Right-click and hold in an empty portion of the Workspace, or on a structure or selection in the Workspace or Sequence Viewer. For example, go to Edit > Pick Mode > Residues and select a residue in the Workspace. Right-click and hold over the selected residue, and a menu of options will appear. From the menu, select Actions > Expand 5 to expand the selection to include atoms within 5 of the initial selected residue. Monitoring Calculation Jobs Click the button in the lower left of the interface to open the Job Monitor panel. This button appears green when jobs are running and appears grey when all jobs are complete. The numbers displayed indicate how many jobs are currently running. Using the Toggle Table The Toggle Table includes a number of shortcut buttons atop a list of entries (rows) currently in the BioLuminate Workspace. Entries can be hidden and made visible by toggling the entry name. Use the buttons to the right of the entry name to act on the corresponding entry: - Actions - Show - Hide - Label - Color All entries in the Toggle Table are included in the Workspace. Before performing a calculation, place only those structures you wish to perform the calculation on in the Workspace. Remove structures from the Workspace: To remove a specifc entry from the Workspace, select > Remove from Workspace. To clear the Workspace, select in the All row and choose Remove Everything from Workspace. Note: Clearing the Workspace does not delete structures (entries) from the project fle; it only excludes them from the Workspace. Working with Projects Create a new project: File > New Project or Ctrl+N Save a project: File > Save Project As; subsequent work is saved automatically to the project fle Open an existing project: File > Open Project or Ctrl+O Close a project: File > Close Project or Ctrl+W Undo/Redo: Edit > Undo, Ctrl+Z, or use the / buttons in the Edit toolbar Working with Multiple Structures Import single or multiple structures: File > Import Structures or Ctrl+I Import a PDB structure: File > Get PDB or click the button in the Project toolbar Clear the workspace: Select > Remove Everything from Workspace in the All row of the Toggle Table or click the
button in the Workspace Toolbar. Clearing the Workspace does not delete your structures (entries); it only excludes them from the Workspace. Superimpose two proteins: Include two proteins in the Workspace, then go to Tools > Protein Structure Alignment
Working with Proteins Generate a 2D diagram of a ligand in a binding pocket: With a protein-ligand complex in the Workspace, select Tools > Ligand Interaction Diagram. Here, select View > LID Legend for a diagram legend. Analyze protein quality: Select in the Proteins Toolbar to view Protein Reports of potential problems with the structure in the Workspace Adjust torsions: Select in the Proteins Toolbar and then select a bond in the Workspace; click and drag the left mouse button to manually adjust the torsional angle View Ramachandran plot: Select in the Proteins Toolbar Changing Molecular Representation Change atom and bond appearance for a given entry: > Preset, or > As > Lines, Sticks, Balls, etc. Change molecular color scheme: > Color by Element, Color by Chain, etc. Modifying and Measuring Structures Adjust distances, angles, and torsions: Edit > Adjust Distances and Angles or click the button in the Edit Toolbar. Structure sculpting: Edit > Structure Sculpting, or click the sculpting button in the Build or Proteins toolbar, then click and drag on an atom in the Workspace. Measurements: Style > Measurements > Pick to Measure to measure a distance. Alternately, press and hold the button in the Labels Toolbar to select to measure a distance, angle, dihedral, or 1H NMR coupling. Then, click on appropriate structures in the Workspace. Using Workspace Styles Apply Workspace Style to a given entry: Style > Apply Predefned Style, or click the button in the Style toobar Edit Workspace Style settings: Style > Predefned Style Settings > Style Settings or click and hold the button in the Style toolbar and select Settings to defne visual styles Automatically re-apply style when contents of Workspace change: Style > Auto Apply Predefned Style or Click the button in the Style toolbar Saving Images Save an image: File > Save Image or select the button in the Toggle Table Save a ray-traced image: Select the button in the Toggle Table Finding and Selecting Structures Find structures or entries: Ctrl+F will display the Find toolbar in the Workspace; use the and buttons in the Find toolbar to traverse matches. Select atoms in the Workspace: Click and hold in the Edit toolbar or go to Edit > Pick Mode and select from Atoms, Residues, Molecules, Chains, or Entries the type of structure you wish to select. Click in the Workspace to select a structure. An entry titled (Selection) is enabled in the Toggle Table. Select atoms in the Sequence Viewer: Choose Edit > Settings > Show Sequence Viewer to turn on the Sequence Viewer. Hover over a residue letter to view the 3-letter residue code and residue number. Select multiple residues using Shift+Click and Ctrl+Click. An entry titled (Selection) is enabled in the Toggle Table. Note: The contents of an entry titled (Selection) are overwritten by the most recent selection. (Selection) entries are also not saved with a project fle. In the (Selection) row, choose > Copy to New Project Entry to create a new entry that will be saved with the project fle. Customizing BioLuminate Many global settings can be adjusted by the menu options at Edit > Settings. Some recommended settings to explore here include Show Sequence Viewer, Preferences, Mouse Actions, and View > Workspace Appearance. Any changes you make to settings are automatically saved for your next BioLuminate session. Getting Help All of our help documentation can be found in the Help drop-down menu.
Help: Search our software documentation using a web browser Knowledge Base: A database of questions that have already been solved by our technical support team Training Videos: Visit www.schrodinger.com/supporttraining/18/32/ Performing Common Operations in BioLuminate 2014