Manuals:GRASP2
From Honiglab_public
Introduction
GRASP2 is a general-purpose graphical program for viewing (and manipulating) sequences, alignments, and molecular structure. It may also be used for searching for and aligning structurally similar proteins, and visualizing molecular surfaces and electrostatic grid potentials. Grid potentials can be calculated beforehand using DelPhi or Qnifft and loaded directly into GRASP2. Various calculations are also available: secondary structure assignment, measuring geometry, detecting hydrogen bonds....
Getting oriented...
GRASP2 is a multiple-document application which means the user can work with more than one group of structures at one time. When you first start the program, you will see a blank workspace where all of this will happen. However, much of the utility of GRASP2 is in being able to compare structures and alignments all in one document and in real-time, and this section is meant to describe the basic layout before going into the actual details.
Typing Ctrl-N, or selecting New from the File menu will bring up a blank document window. Once a blank document is in view, a new structure can be loaded into the document by using Ctrl-O, or selecting Open from the File menu. From here, a PDB file can be selected. Once loaded, the structure will be displayed in Wireframe in the document window although this can be changed by the user. See the section Changing the molecular representation below.
After this happens, the Subset sidebar on the left and the Sequence panel on the bottom will fill with new information detailing the chains, ligands and other heteroatoms in the Subset sidebar, and the molecular sequence in the Sequence panel. In general, right-clicking on the items in the Subset sidebar or Sequence panel will open up popup menus that are available for manipulating each sequence or subset. The topbar containing the Subset box, Style, Color and Action menus allows you to quickly access subsets and change molecular visualizations for selected subsets.
The sections below describe the different methods that can be used in GRASP2. The mouse controls are described in the section Viewing structures.
Basic operations and methods
Structures
Loading structures
Structures can be loaded into GRASP2 using File->New and then using File->Add to select a PDB file to the new window, as described in Getting Oriented. In addition, PDB files can be loaded directly into a new window using File->Open. Also, a project file (or .tpr file) containing one or more structures can be loaded using the File->Open menu. Project files are described further below.
When a structure is loaded into the window, all of the chains, ligands, and other heteroatom groups will be added to the subset window, as well as a list of the Default Sequences. Proteins and nucleic acids will be labeled with their chain IDs in the window (an underscore is used if the chain ID is blank). These objects can be selected later so that their viewing options can be changed as described in Changing the molecular representation.
Viewing structures (Using the mouse & menu options)
If you have used rasmol or other molecular viewers to examine structures, using the mouse to change the view of the structure should be familiar, but the operations might be activated by slightly different mouse-clicks. These are described below:
- Mouse controls
- Hold Left Mouse Button - Rotate view
- Hold Left Mouse Button + Shift - Translate view
- Hold Right Mouse Button - Zoom in (down), Zoom out (up)
- Click Right Mouse Button - Identify atom under the mouse pointer in the Status bar
- Click Right Mouse Button + Ctrl - Open dialog box to Calculate distances, angles, dihedrals.
- Menu controls
- Edit->Background - Change the background color
- Edit->Graphics Options - Change how Spheres, and Balls and Sticks are drawn. Manage color scales.
- Edit->Color Options - Manage coloring options
- View->Recenter - Resize the panel to show all molecules and recenter the point of rotation
- View->Stereo - Switch to (cross-eyed) stereo view
- View->Anaglyph - Switch to anaglyph stereo view
- View->Projection mode - Switch from parallel to perspective projection modes
Changing the molecular representation
GRASP2 displays several different molecular (or atomic) representations, or Styles, for molecules. These are: Wires, Ball and Sticks, Spheres, Worm, C-alpha (CA) Trace, CA Wires, Bar, Cylinder, Ribbons, and Boxes.
Different molecular representations can be added, changed or deleted for every molecule in the display. In addition, different subsets of atoms or residues can be defined, so that changing the molecular representation only affect those subsets.
Changing the representation of a molecule in the viewing panel requires:
- Selecting the subset to be displayed in either the subset or sequence window.
- Selecting the Replace, Add or Delete in the Action Toolbar menu.
- Selecting the Style from the Toolbar menu to be Replace, Add to or Delete from the view.
- Sometimes, if the molecule does not immediately come into view, it is helpful to Recenter the view (View->Recenter).
Also, instead of using the Toolbar menu in steps 2-3 above, selecting Style after right-clicking a selected subset will also complete this task. Changes in color can also be activated using the Toolbar menu or in the Style dropdown menu.
Calculate distances angles and dihedrals
Holding Ctrl and right-clicking on an atom in the main window will select that atom and place it in the Atom 1 field of the Calculate dialog box. To calculate a distance, select one more atom by Ctrl-right-clicking, filling up Atom 2. To calculate angles, select two more atoms this same way, filling up Atom 2 and Atom 3. To calculate dihedrals, select three more atoms, filling all four Atom fields. The calculated values will always appear in the lower left corner of the dialog box.
Performing structure alignments
Structural alignments are constructed by selecting two or more proteins in the Subset panel, right-clicking to access the Right Mouse Button menu, and selecting Align->Structures. The alignment will be performed using the algorithm published in the References.
This will open a menu that will allow you to specify the parameters for the structure alignment algorithm. To align the two structures using all the default parameters, click Align at the bottom. The two structures will be immediately aligned in the main view, and a new sequence alignment object will be added to the Subset panel. The sequence alignment itself will be displayed in the Alignment panel.
A nice feature of Structure Alignment in GRASP2 is the option to Link the positions of other molecules in GRASP2 to the alignment of the structures. For example, if Protein A is bound to a ligand, then it is possible to Link the ligand to Protein A, align Protein A to B and this will rotate the ligand along with A, allowing you to see the position of the ligand relate to B after the alignment.
After aligning two proteins, it is possible to obtain the RMSD and Protein Structure Distance (PSD, see References). Left-select two proteins in the Subsets panel of the Structure Alignment window. PSD and RMSD will be displayed below the Subsets and SSEs panels.
Performing database searches (Skan)
Saving views in the window
Saving a view allows you to store the orientation of selected molecules and subsets, surfaces, coloring and style in the main window inside a View object in the Subset panel so that you can go back to the same view by Applying it later on. To save a view, select View->Save. To go back to that view later, right-click on the View object and select Apply.
Saving project files
Saving a project file will save all the molecules that have been currently loaded into the main window so that when the project file is opened later, all of the structures will be in the same place in the main window. Also, any surfaces, sequences, graphical views and structure alignments that have been created will also be loaded. To save a project file, select File->Save or File->Save as from the main menu.
Manipulating Subsets
Key words in creating subsets
- Key words and symbols
- object
- range
- atom
- and/or/not
- ()
Defining subsets from the Toolbar
Defining subsets from the Sequence panel
Surfaces
GRASP2 displays four different types of surfaces: molecular, solvent accessible, Gaussian, and van der Waals (VDW). The molecular surface is the one most commonly visualized and represents the region around a molecule that can be accessed by the surface of a water molecule. This surface encloses the VDW surface of the molecule, but also any region (called re-entrant) that water cannot penetrate because the space is too narrow. All four kinds of surfaces can be displayed.
Displaying surfaces
To draw the surface around a molecule or subset of atoms, right-clicking over the appropriate Subset in the left panel, access the Right Mouse Button dropdown menu, and select Surface. From here, one of the four kinds of surfaces can be calculated for display.
Once the surface is selected, it will be displayed immediately in the main view, and a Surface Object will appear in the Subset panel. The properties of the surface being displayed can be changed by right-clicking the Surface Object and selecting Properties. Each surface can be hidden by selecting Hide from the same menu, or deleted altogether with Delete.
Using the Properties window, colors can be selected for different parts of the surface, or according to a user-defined subset. This is selected in the top panel. The Coloring method can be selected from the middle panel. Several coloring options are available, which are mostly the same as those that can be chosen for different molecular representations (see Changing the molecular representation). The additional option of coloring by potential is described further in Mapping potentials to the surface.
The level of transparency can also be set for each surface in the bottom panel.
Loading electrostatic grid potentials
Phimaps containing the electrostatic grid potentials for a given molecule can be calculated independently of GRASP2 (by programs like Delphi and Qnifft) and imported into GRASP2 after. Once loaded into GRASP2, isopotential contours can be displayed, or the electrostatic potentials can be mapped onto the surface of a molecule and displayed in color.
Phimaps are loaded by selecting File->Load phimap->Insight format. Immediately after the phimap is loaded, a Phimap object will appear in the Subset panel.
Right now, only the Insight format is supported, so make sure you specify this output format for the phimap in Delphi or Qnifft! To find out more about how to use Delphi, visit the Delphi manual. A good place to find out how to use Qnifft can be found in this tutorial. A quick summary of the relevant parameters is given below:
- Delphi
- out(phi,file="phimap.grd",format=BIOSYM) - Output an Insight (Biosym) readable phimap
- Qnifft
- phi_output_file=phimap.grd - Generate a phimap
- insight_format=t - Make sure this is set to t (true)!
Displaying isopotential contours
Right-clicking on the Phimap object will give access to an option to display Contours. Select Contour on the menu to open a window that will ask for the minimum value of the electrostatic potential contour (Minimum), the number of contours to generate (# of steps), and the increment between each contour (stepsize). Clicking OK will generate the contours and display them in the main view.
When the contours are first displayed, they will be Solid. To change this property, right-click the Potential Contour (PC) objects and select or deselect Mesh. PC objects are added to the Subset panel when the contours are first created.
Mapping potentials to the surface
Mapping the electrostatic potential to the surface of a molecule involves the following steps:
- Load the electrostatic grid potentials
- Create a surface for the molecule
- After this, a Molecular Surface (MS) object will be added to the Subset panel. Right-click to access its Properties menu item.
- In the Edit Surface Properties window, select Set colors for: Entire surface. This should be the default setting.
- Under Color Method: Entire surface, select Potentials.
- Adjust the Color scale options if necessary and hit Apply to execute.
The surface should now be colored according the potentials in the phimap.
Sequences and Alignments
Loading sequences or alignments
Manipulating sequences
Manipulating alignments
Merging sequences and alignments
Generating profile-profile alignments (HMAP)
Calculations
Assigning secondary structure to sequence
Calculating hydrogen bonds
Perturbing the structure
Menu Items
- File
- Open
- Download
- Add
- Save/Save as
- Save image
- Load sequence
- Load SSE list
- Load HMAP profile
- Load phimap
- Print/Print preview/Print setup...
- Close
- Exit
- Edit
- Background
- File locations
- H-bond parameters
- Graphics options
- Color options
- Structure
- Build
- Add a residue to chain terminal
- Add missing atoms to residue
- Mutate a residue
- Rotate a dihedral angle
- Sample
- Sidechains
- SSEs
- Calculate
- H-bonds/Salt bridges
- Compare
- View
- Toolbar
- Status bar
- Recenter
- Stereo
- Anaglyph
- Projection
- Perspective
- Parallel
- Save
- Set world focus
- Residue cylinder
- Program log
- Window
- Split
- Limit to pane
- Save size
- Tile
- Cascade
- Help
- About vctroll...
Shortcuts
Global actions
| Shortcut____ | Function________________________________________________ |
|---|---|
| a | Select all atoms. |
| CTRL-A | Set Action to Add for changing styles. |
| CTRL-D | Clear the display window. |
| CTRL-E | Set Action to Delete for changing styles. |
| CTRL-O | Select Open from the File Menu. |
| CTRL-P | Select Print from the File Menu. |
| CTRL-S | Select Save from the File Menu. |
| CTRL-R | Set Action to Replace for changing styles. |
| CTRL-W | Set display style to Worm for displayed structures. Color will be assigned differently to each structure. |
Color actions
To activate these items, press 'c' and then one of the following letters.
| Shortcut____ | Function________________________________________________ |
|---|---|
| a | Maroon |
| b | Blue |
| c | Color atoms by CPK convention |
| g | Green |
| h | Color by chain |
| m | Magenta |
| n | Color by rainbow, from N- to C-terminus |
| o | Orange |
| p | Plum |
| r | Red |
| s | Select a color from a dialog box |
| t | Turquoise |
| w | White |
| y | Yellow |
Style actions
To activate these items, press 's' and then one of the following letters.
| Shortcut____ | Function________________________________________________ |
|---|---|
| w | Worm |
| i | Wires |
| b | Ball and stick |
| s | Spheres |
| c | C-alpha wires |
| t | C-alpha trace |
| r | Ribbon |
| x | Boxes |
Installing
Bugs
Please report bugs to Donald Petrey at Columbia University.
References
Petrey, D. and Honig, B. (2003)
GRASP2: Visualization, Surface Properties, and Electrostatics of Macromolecular Structures and Sequences.
Methods in Enzymology. 374: 492-509
