This chapter describes several mechanisms for displaying and studying structures as solid models. Read this chapter to become familiar with the options for visual representation of your structures.
Some of the visual representations can be manipulated as objects in QUANTA (solid models), some are for display purposes only (raster and raytrace images), and some can be printed as hardcopy (artist plots).
Solid Models in the Draw menu of the main menu bar provides a number of rendering styles for creating space-filling models. Depending on your workstation, you can display solid models in the viewing area of the Molecule window or in a separate Solid Model window that opens when you make a solid model selection. Displaying solid models in the viewing area requires RGB graphics. Machines with color map graphics use the Solid Model window. The interface for generating solid models is the same for both display mechanisms.
Solid models generated in the viewing area are treated as graphical objects. When a solid model is selected, the Object Management Table is displayed, listing the model as an object. Only one solid model object can be applied to a structure at a time, but several objects (with different names) can be simultaneously displayed.
Different rendering styles can be used in different parts of the structure. Different rendering styles also can be applied to different structures displayed at the same time, but stored in separate MSFs. For more general information about manipulating and displaying graphical objects, see Chapter 6.
The rendering styles available in the Solid Models pull-right menu include:
Table 35 lists and briefly describes all the selections on the Solid Models pull-right menu.
Additional modeling choices are available in the Solid Schemes and Utilities palette, opened when you select Selection Tools from the Solid Models pull-right menu. The Solid Display palette is also opened. Tables 36 and 37 list the selections on these palettes and provide a brief description of each.
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Nothing
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Stick
| Renders subsequently selected atoms using a stick model. Standard default display |
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Ball and Stick
| Renders subsequently selected atoms using a color-coded ball and stick model. |
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Liquorice
| Renders subsequently selected atoms using a liquorice model. |
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VDW
| Renders subsequently selected atoms as spheres with radii proportional to the van der Waals radii in the atom type parameter file. |
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Sheet
| Renders subsequently selected atoms in a protein using a thick ribbon model of protein backbone. |
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Ribbon
| Renders a designated portion of a molecule using a thin ribbon model. |
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Helix
| Renders a helical portion of a molecule using a thick ribbon model. |
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Cylinder
| Displays a cylinder through the helical portion of a molecule |
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Secondary Structure
| |
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Parameters
| Opens a dialog box allowing changes in solid model parameters. Same as Settings selections in the Solid Model menu. |
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Translucency
| Opens a dialog box for setting translucency of solid models. |
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Read Selection Commands
| Reads commands from file.ssd and updates the viewing area to reflect the new set of commands. |
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Append Selection Commands
| Appends the current .sol with a set of commands from another file, file.ssd f and updates the viewing area to reflect the new combined set of commands. |
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Save Selection Commands
| Saves the current set of commands to a new file.ssd. Only available when One MSF is selected in the Display Atoms palette. Selections can be saved for only one MSF at a time. |
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List Selection Commands
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Edit File Manually
| Allows a .dsf file to be manually edited. A new window is opened which uses the vi editor for editing the file1. |
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Help on Commands
| Provides a list in the textport of display selection commands that can be used from the keyboard. Each entry includes a short example. |
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1You can change the default editor by using the UNIX setenv command before QUANTA is started. The syntax is: setenv EDITOR name_of_text_editor.
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When a solid model is displayed in the QUANTA viewing area, the model can be manipulated using the techniques that you use for any structure. For example, you can perform global transformations using dials on the Dial Emulator or the mouse and keyboard.
When you move a structure to which you have attached an object, the object, by default, is hidden during the movement. This helps speed up manipulation, particularly of complex molecules.
If you want to the object to be visible throughout the manipulation, open the Preferences menu, select Suppress Objects, then select Off from the pull-right menu that opens. All objects will be displayed during movement of the structure until you change the preference.
Solid model display in the viewing area requires that a machine use RGB graphics. Machines with color map graphics use the Solid Model window. The interface for generating solid models is essentially the same for both display mechanisms. The difference is that with machines using the Solid Model window, solid model graphical objects are displayed in this window, not as an integrated display in the Molecule window.
If your machine uses the Solid Model window, models are manipulated by placing the cursor in the window and using standard cursor-keyboard combinations for translation and rotation. Structures containing more than 15 atoms may require a considerable period of time to redraw in the new orientation.
The size and position of the Solid Model window can be changed using the standard workstation window manager. When a window is open, the left mouse button can be used to display a popup for modifying various aspects of the solid model display. Selections are made from this menu (and other menus called by this menu) by using the right mouse button.
Table 38 lists and briefly describes the selections in this popup. Tables 39 and 40 list and describe the selections in submenus of the Solid Model window popup.
Complete the following exercise to become familiar with creating and modifying solid models. This exercise uses the structure mypeptide, built in the Creating a Peptide section of Chapter 4. It assumes you are working on a workstation with RGB graphics.
Display the File menu and select the Open function. Select mypeptide.msf from the File Librarian dialog box scrolling list. Select the Replace option and then the Open button.
2. Choose a solid model to display.
Display the Draw menu and select Solid Models. From the pull-right menu that opens, select Ball and Stick. The structure mypeptide is displayed in the viewing area using the ball and stick model. The Object Management Table is displayed listing the object SOL_object.
3. Select another solid model rendering.
Display the Draw menu again. Select Solid Models and then select Liquorice from the pull-right menu. The mypeptide structure changes to a liquorice model. There is no change in the Object Management Table.
Select the Displayed column for SOL_object. The text changes from yes to no, and the structure returns to the standard stick display.
Select the Displayed column again. The text changes from no to yes, and the liquorice model is displayed again.
4. 4. Change solid model settings.
In the Modeling palette, select Hydrogen Bonds
From the Draw menu, select Solid Models, and then select Settings from the pull-right menu. In the dialog box that opens, enter the value:
Thickness of Liquorice Models: 0.4
Select the Redraw button and the display changes to reflect the changes you have made.
Return to the Draw menu, select Solid Models, and then select Ball and Stick from the pull-right menu. The Object Management Table remains unchanged.
From the Draw menu, select Solid Models, and then select Selection Tools from the pull-right menu. The Object Management Table is removed, and the Solid Display and Solid Schemes and Utilities palettes are opened.
In the upper-right corner of the viewing area, modeling choices are presented in a color-coded list, which duplicates the choices in the Solid Schemes and Utilities palette.
The molecule display changes to a red stick model. (The red color indicates the Ball and Stick model has been selected.) In the viewing area list, Ball and Stick is marked with a *, and Ball and Stick is checked and highlighted in the Solid Schemes and Utilities palette. No model is actually displayed until you exit Selection Tools.
Select Clear from the Solid Display palette and Nothing from the Solid Schemes and Utilities palette. Nothing is checked and highlighted and the structure turns pale green.
7. Select several solid renderings for different parts of the structure.
From the list in the upper-right corner of the viewing area, select Ribbon . Thin Ribbon is checked and highlighted in the Solid Schemes and Utilities palette.
In the Solid Display palette, select Protein Backbone and the structure's protein backbone is displayed in purple.
From the list in the upper-right corner, select VDW Spheres.
From the Solid Display palette, select Pick Residue and the message line reads:
Select the atoms to be type VDW. Pick atom to select residue.
Pick an atom in the residue of your choice and the residue turns white.
From the Solid Display palette, select Finish and the Selection Tools palettes are closed. The structure is displayed in the viewing area with a pale green ribbon backbone and a single residue modeled as van der Waals spheres. The Object Management Table reopens listing SOL_ object.
Select the Delete column of the Object Management Table. The structure returns to a standard stick display and the Object Management Table closes.
Cartoons can be generated for different types of molecules including proteins and nucleic acids. To generate a cartoon from a protein file, the secondary structure must be defined. If you have a protein without a defined secondary structure, use the Protein Design application in the Applications menu to define the structure before you generate a cartoon solid model.
Complete the following exercise to become familiar with creating protein and DNA cartoons. This exercise uses the structures complex_dna and complex_prot. To copy the MSFs into your QUANTA tutorial directory, issue this UNIX command while in that directory:
> cp $QNT_ROOT/userguide/complex_*.msf .
The structures represent a modeled interaction of a modified DNA with a protein. Complex_prot.msf already contains secondary structure information for the molecule.
1. Open complex_prot.msf and complex_dna.msf.
From the File menu, select Open and a File Librarian dialog box opens.
From the dialog box scrolling list, select complex_prof.msf and then complex.dna.msf.
Select the Replace option and then the click the Open button.
2. Apply Solid Selection Tools.
From the Draw menu, select Solid Models. From the pull-right menu that is displayed, select Selection Tools. The Solid Display and the Solid Schemes and Utilities palettes are displayed.
3. Set up protein cartoon parameters.
From the Solid Display palette, select One MSF... and a dialog box opens. From the dialog box scrolling list, select complex_prot.msf.
From the Solid Schemes and Utilities palette, select Parameters... In the Solid Models Settings dialog box that opens, click the Reset to Default Values button. This sets the appropriate parameters for protein cartoon drawing.
If you want alpha helices to be drawn as cylinders, check the Draw Helices as Cylinders option, and then click the OK button.
4. Select the protein cartoon.
From the Solid Schemes and Utilities palette, select Secondary Structure .
Then from the Solid Display palette, select All Atoms. The protein backbone is colored to show the zones that are sheet, ribbon, helix, or cylinder.
5. Set up DNA cartoon parameters.
Select One MSF... from the Solid Display palette and a dialog box opens.
From the dialog box scrolling list, select complex_dna.msf.
From the Solid Schemes and Utilities palette, select Parameters... and the Solid Models Settings dialog box opens.
Enter these values to optimize the settings for DNA display:
Atom defining path of ribbon: C1'
Maximum Distance Apart of Atoms: 7.0
Offset of ribbon from guide atom: 1.
Helix Thickness: 0.8
Ribbon Width: 0.6 Thickness: 0.6
Draw "rungs" between double-helix "ladders"
From the Solid Schemes and Utilities palette, select Helical Ribbon.
From the Solid Schemes and Utilities palette, select All Atoms and the C1' guide atoms are displayed in purple.
From the Solid Display palette, select Finish and a solid model graphical object is displayed for each MSF. Ribbons are colored according to the color of the guide atoms, in this case, the default color, light green.
The Object Management Table is displayed, listing an object for each structure.
From the Draw menu, select Color Atoms. Then from the pull-right menu that is displayed, select Selection Tools. The Color Schemes and Utilities and the Color Atoms palettes are displayed.
From the Color Schemes and Utilities palette, select Color by Secondary Structure.
From the Color Atoms palette, select Pick Segment, and then pick an atom in one of the DNA chains.
From the Color Atoms palette, select Next Color Number, and then pick an atom in the other DNA chain.
9. Display the cartoons with the new color scheme.
From the Color Atoms palette, select Finish. The protein should now be colored according to the secondary structure, with the DNA chains blue and red.
From the Draw menu select Solid Models. From the pull-right menu that is displayed, select Redraw Model, and the solid models are re-created using the new color scheme.
10. Display the solid models only.
To show just the solid models without the usual vector bond display, open the Draw menu and select Manage Display.
From the dialog box that opens, toggle Bonds off. Then click the OK button.
To restore the display of bonds, press the <F10> key.
11. Return the structures to their original display.
In the Object Management Table, select the Delete cell for each object and the objects are removed from the viewing area.
From the Draw menu, select Color Atoms, and then select By Element from the pull-right menu that is displayed. The structures are colored by element.
The Solid Surfaces item on the Calculate menu offers the following choices on the pull-right submenu:
]Calculates a solid surface for each currently displayed MSF using the current settings and displays the surface. Each surface occupies a graphical object, so their display can be toggled or they can be deleted using the Object Management table in the usual way. (For more information about the Object Management table, see QUANTA: Generating and Displaying Molecules, Chapter 6.) The surface objects are named SUR_msfname. To create an alternative surface for an MSF while keeping an existing one, click its name in the Object Management table and change its name from this default.
The surface calculation can be aborted before completion by clicking the mouse.
Displays a dialog box giving the options for calculating and displaying solid surfaces. The options are:
If you choose to proceed with the calculation rather than just setting the preferences, it will be displayed after calculation and the display adjustment palette will be entered (see below). This allows alteration of the surface display even if it hasn't been saved to file.
If you opted to save surface files, the surface can be recreated in different styles. A palette is displayed with the following tools:
Each vertex is colored like the nearest atom.
The surface for each MSF is colored differently.
The electrostatic potential at the surface is calculated, using the current atomic charges. A dialog box appears that allows you to control the energy range and color numbers for the color ramping.
Allows you to re-display the electrostatic surface with different ramping without recalculating it.
Displays a dialog box that allows control of the tonal color ramping (for example, the blue to red to white that is used for electrostatics).
Displays a dialog box that allows you to control the spectral color ramping (for example, red to blue to green).
Resets the color values to default settings.
Make the surface opaque. Nearly Opaque Make the surface nearly opaque.
Make the surface nearly translucent.
The quality of the solid surface representation depends on the graphics hardware. Even with base-level graphics, you can improve the display using the following options:
Toggles between two alternative pattern sets to be used for the semi-opaque surfaces.
Sets the system to single-buffer mode when the molecule is stationary. This allows all the available bitplanes to be used for rendering the picture. Double-buffer mode is resumed when the molecule starts to move. Inevitably, you will see the picture being redrawn in between, so this option is not recommended for normal use, rather it should be turned on prior to taking photos, etc., and turned off afterwards.
Turns on or off backface polygon removal for the solid surface. This has the effect of removing any polygons for which the face (normal) of the polygon is facing away from the viewer. This has the effect of additional clipping, allowing buried molecular surfaces to be clipped for viewing purposes.
Raytrace is a pull-right menu in the Draw menu that contains several options for creating a pseudo-3D rendering of structures displayed in the workspace. The rendering employs both highlight and shadow detail to provide a better defined image. Ray-traced movies can be scripted.
This option executes the original raytrace program that has been available with QUANTA for many years, which produces an image of a van der Waals representation of the currently displayed atoms.
1. Display the 3D rendering of a structure.
Display the Draw menu and select Raytrace/Original Raytrace. A ray-traced image of a van der Waals representation of mypeptide.msf is generated in the Ray Tracing window.
2. Remove the rendering and return to original display.
With the cursor is in the Ray Tracing window, click the left mouse button and the Ray Tracing window closes.
This option executes the Rayshade program (see below) to produce a ray-traced image of the currently displayed solid graphics objects (e.g. van der Waals, protein cartoon, or solid surfaces). QUANTA generates an intermediate file called run.rayshade containing commands and graphics primitives for the rayshade program. This is run and the output placed in a file called r.rle.
On requesting a Rayshade Solid drawing, a dialogue box is displayed which prompts for the size of the image to be produced and whether a background plane is to be included in the image. Images of 300 pixels should be generated to start with, since generation can take considerable time.
The Rayshade program is in the public domain and can be obtained over the internet from several sites. Contact your Accelrys support office for information on how to obtain the program.
The Plot Molecules menu in the File menu is used to define and create plot files for the generation of hard copies of structures. The plots can be previewed on the screen before hardcopies are generated.
The types of output files are:
Uses an external program to produce ball and stick, van der Waals, or user-defined representations of structures for publication quality plots. The User-defined option offers a list of commands that define how the structure(s) can be rendered.
Creates a plot of the molecule using the currently stored information about bonds, labels, IDs, hydrogen bonds, and other pertinent parameters. Graphic objects are not plotted in this mode.
Creates a plot of all the currently displayed vector, dot, and text information in the graphics window. The image is clipped as seen on the screen. This option is only available on Silicon Graphics workstations that support the feedback buffer mechanism used.
Creates high-quality hardcopy output of molecular structures including protein cartoons.
Available only on certain Silicon Graphics workstations, creates an image file of the current screen and converts the image to PostScript format. The UNIX programs scrsave, iflip, and tops must be in your path.
Creates a PostScript plot of any solid models or surfaces.
The first five of these plottypes are created by selecting Generate from the Plot Molecules menu. Table 42 lists the plot options available in the Setup Hard Copy Plot of Molecules dialog box.
The MolScript and Color Screen Image create PostScript plot files directly. These may be previewed using the Preview selection in the Plot Molecules menu; the function automatically detects if the file is in PostScript format and if so uses the xpsview program instead of the usual QUANTA preview program.
The other plot types first produce a QUANTA plot file, which is a general-purpose binary file containing graphical information.(Please see Appendix C in the Basic Operations guide for further details). A dialog box is then displayed giving a choice of plot disposition options.
You can also use the Preview selection in the Plot Molecules pull-right menu (under the File menu) to view the contents of a QUANTA plot file on the screen. Or you can use an interactive figure editor in the user_group_files area to convert the file to a format accepted by the xfig program distributed by Silicon Graphics.
Table 43 lists and briefly describes the options in the Plot Disposition dialog box.
Producing a hardcopy plot is a two-stage process. The first stage involves specifying the type of plot required. The second stage involves specifying how the plot is to be output.
Complete the following exercise to become familiar with the procedure for producing hardcopy plot.
1. Produce a ball and stick artist plot with a scale of 5 mm per angstrom.
Display the File menu and select Plot Molecules. From the pull-right menu that opens, select Generate. In the Setup Hard Copy Plot of Molecules dialog box that opens:
Artist Plot
Ball and Stick
Current View
Click the OK button. After a short wait, the Plot Disposition dialog box offers options for viewing and printing the plot.
Click the OK button and the ball and stick rendered peptide molecule is displayed in the QUANTA Preview window. Information about the rendering is displayed at the bottom of the window.
Move the cursor inside the QUANTA Preview window and click the left mouse button. The window is removed from the screen and the Plot Disposition dialog box opens.
At this point, you can return to the Setup Hard Copy Plot option in the Molecules dialog box to alter the appearance of the plot. If you do so, select the Regenerate Plot option after making your changes. Or you may create output of the plot displayed on the screen.
2. Create a PostScript File using ball and stick rendered peptide.
From the Plot Disposition dialog box, select the options:
PostScript Format
Translate as Color and Texture (under PostScript options)
Click the OK button and a File Librarian dialog box opens.
Enter the text mypeptide and click the Save button to save the PostScript file as mypeptide.ps. The file is created and you are returned to Molecular Modeling mode.
3. Output hard copy of a PostScript (.ps) file.
The procedure for sending the .ps file to a particular PostScript output device depends on how the computer is set up, network hardware and software being used, and the output device. Please consult with your system administrators.
4. Generate a user-defined output file.
Display the File menu and select Plot Molecules. In the Setup Hardcopy Plot of Molecules dialog box that opens, select the option:
Click the OK button and a dialog box opens to accept commands specifying how the structure is rendered.
Enter the text Help in the data entry field to view a list of available commands in the textport. These commands, their form, and a brief description of each are listed in Table 44.
MolScript is a program for creating molecular graphics in the form of PostScript plot files. Possible representations are simple wire models, CPK spheres, ball-and-stick models, text labels, and Jane Richardson-type schematic drawings of proteins, based on atomic coordinates in various formats. Color, grayscale, shading, and depth cueing can be applied to the various graphical objects.
The QUANTA interface to MolScript generates the input script and coordinate files to reproduce as nearly as possible the current representation. Objects rendered include bonds, solid models, hydrogen bonds, distance monitors, labels, and atom IDs.
Quanta supports several versions of Molscript that have a few differences in capability and keywords. Please make sure you fill in the correct version number in the MolScript options dialog.
The interface is accessed by using the function Plot Molecules Æ Generate on the File menu. This displays the usual Setup Hard Copy Plot of Molecules dialog box, which includes a MolScript Plot radio button. When this is used, a dialog box is displayed containing the MolScript interface options.
Specifies which version of Molscript you have installed.
The interface produces two files, filename.pdb containing the molecular coordinates, and filename.in containing the MolScript commands. Running the program produces the PostScript file filename.ps or filename.eps.
This is used to control the maximum bond distance allowed in ball-and-stick plots. The default 2.1 Å is suitable for proteins containing disulfide bridges but no hydrogen atoms; if hydrogen atoms are present, a smaller value is needed to prevent the hydrogen atoms from being bonded together. Vector bonds are generated using the LINE command, so that the exact bonding generated by QUANTA can be replicated regardless of this setting.
MolScript allows for optional smoothing of thin ribbons. This can make for a clearer diagram, but should be avoided if sidechains are also displayed.
This can sometimes make for a clearer diagram.
Changes the color settings to be optimized for the drawing of solid models.The plot always has a white background regardless of the QUANTA background color.
Allows the input files to be retained - expert users may want to manually adjust the input and rerun MolScript. If this option is unchecked, then the input files will be deleted if MolScript is run successfully.
This option causes the resulting PostScript plot to be displayed with the xpsview viewing program. Xpsview or an alias pointing to it must be in your path.
If both solid models and vector bonds are displayed on screen, then both are included in the MolScript plot. Remember that vector bonds can be rapidly toggled using function key <F10> if the default key bindings are set up. Otherwise, enter the commands HIDE BOND and SHOW BOND.
When the OK button is clicked, the input files are created and MolScript is run.
The MolScript program must be obtained from its author, Dr. Per Kraulis.
Per Kraulis, Ph.D phone: +46 (8) 695 78 34
Pharmacia & Upjohn, Inc. fax: +46 (8) 695 40 82
PPC Sweden Research, N62:5 e-mail:
S-112 87 Stockholm krpx@sgikrpe.sto.se.pnu.com
SWEDEN or p.j.kraulis@bioc.cam.ac.uk
or molscript@bioc.cam.ac.uk
The software is provided under license - details from Per Kraulis.
In publications, you must refer to:
Per J. Kraulis "MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures" J. Appl. Crystallog. 24 946-950 (1991).
This chapter describes several mechanisms for visually representing structures. Some of the visual representations can be manipulated as objects in QUANTA (solid models), some are for display purposes only (raster and raytrace images), and some can be printed as hardcopy (artist plots).
The Solid Models function in the Draw menu provides several styles for rendering space-filling models. Depending on your workstation, solid models are displayed in the viewing area of the Molecule window or in a separate Solid Model window
Solid models generated in the viewing area are treated as graphical objects. Only one solid model object can be applied to a structure at a time, but different rendering styles can be used in different parts of the structure. Different rendering styles also can be applied to different structures displayed at the same time but stored in separate MSFs.
The rendering styles available in the Solid Models pull-right menu include: ball and stick, van der Waals, liquorice, and cartoon models.
Raytrace in the Draw menu is a selection that creates a pseudo-3D rendering of structures. The rendering employs a van der Waals model and uses the default atom sizes and colors that are set up before Raytrace is selected. It employs both highlight and shadow detail to provide a better defined image. The image cannot be manipulated.
The Plots selection in the File menu is used to define and create plot files for generating hard copies of structures. The plots can be previewed on the screen before hardcopies are generated.