DS ViewerPro |
This chapter discusses how to:
The fourth lesson briefly shows some of the ways you can visualize DNA, and the fifth lesson uses pyrite to highlight DS ViewerPro's crystal-handling capabilities.
If your lesson is interrupted
Each of these lessons is designed to be worked from step 1 to the end without quitting DS ViewerPro or leaving the sequence of lesson steps. You can easily handle an interruption, however, by properly saving your work in a new file and loading it again when you are ready to continue.
To save a DS ViewerPro document (which in these lessons typically contains only one molecule), follow these steps:
This can be the QuickStart folder, where the original files are stored, or another folder of your choosing.
This file name should differ from the original file's name, so you are sure not to overwrite the file that everyone needs to begin the lesson.
When you are ready to resume a Quick Start lesson, simply reload your molecule and continue from the point where you stopped.
In this first Quick Start lesson, we will load a small and relatively simple molecule, luciferin, into the DS ViewerPro and see some of the display options. We'll investigate the sketching capabilities of DS ViewerPro by building our own model of luciferin and exporting it to various formats.
Starting DS ViewerPro
The DS ViewerPro window opens with no molecule loaded. The Menu bar displays six menus and the Toolbar lies across the top of the window. On the left-hand window frame, the Tool palette appears.
Start the DS ViewerPro program by double-clicking the DS ViewerPro program icon.
Alternately
DS ViewerPro can be started several ways that simultaneously load the molecule of interest:
Select the Open command from the File menu. In the file browser, navigate to the QuickStart folder. Highlight the filename Luciferin.msv by clicking on it and then click the Open button. |
The DS ViewerPro uses color to denote the element types of atoms. The DS ViewerPro uses gray for Carbon, white for Hydrogen, red for Oxygen, blue for Nitrogen, and a mustard-yellow for Sulfur. You can change any of the default element colors with the Tools / Element Properties command.
Adjusting display styles
Now, try the different controls on the toolbars.
Next, try the other display effects on the Tool palette. Later, we will try the sketching tools.
Click the Torsion tool, then click on the central C-C
bond and drag. Torsion ![]() |
Selecting and editing
Next we will experiment with the selection modes and editing commands.
Click the Selection tool. Drag a rectangle around the whole molecule, making sure you don't miss any atoms or bonds. |
The whole molecule becomes selected. This is indicated by all the atoms and bonds turning yellow.
While the molecule is selected, go to the Edit menu and select the Properties... command. |
The Molecule Properties window opens, providing such information as number of atoms, molecular formula, molecular weight, and molecular volume. Depending on what type of object you select before issuing the Edit / Properties... command, this window customizes to display the relevant information.
Now we will make a copy of the molecule and paste it into the document.
Select the Edit / Copy command. |
The selected molecule is copied to the Clipboard. Now we will paste the copy back into the document and investigate how selection and commands interact.
Note that the luciferin molecule is still selected. Click the Paste command in the Edit menu. |
The window does not appear different, because the pasted molecule is coincident with the original one. The original molecule is deselected and the pasted one is selected.
Click the Translate tool on the Tool palette. Then click and drag the mouse across the document window. |
Both the selected and deselected copies of luciferin follow the movement of the mouse. Use the <Ctrl> key to alter this behavior:
With the Translate tool still selected, hold down the <Ctrl> key while dragging the mouse across the document window. |
Now only the selected copy of luciferin moves with the mouse, and the coincident molecules are now separated.
Changing your view
While one molecule is still selected, we will see how the Fit to Screen, Reset Rotation, and Center View commands work on this pair of molecules.
You should observe the following series of results:
Preparing the document
We will be working with two documents -- one holding the loaded luciferin and one holding our sketch.
The double-click selects the group in the molecule that contains the bond or atom on which you double-click; in this simple case, that means selecting the whole molecule.
You should now have a centered view of luciferin, displayed in the Line style.
Adding labels
Now we add labels to assist us while sketching our copy of luciferin.
Atom name labels are displayed next to each atom. These labels will assist you in assigning elements to atoms in your luciferin sketch. Now we want to adjust the view of this guide molecule.
Use the Rotate tool to arrange the luciferin molecule in a position that best shows its atoms and bonds. |
Sketching a molecule
Your DS ViewerPro windows should appear similar
to this:
Use the File / New command to create an empty document. Go to the Window menu and select Tile Vertical.
Building rings
Now it is time to start sketching.
Click in the Molecule2 document to make sure it is active, then click on the Ring tool. In the document window, click the mouse button once to create a 6-membered ring. |
The Ring tool reports the size of the ring it is drawing, "Size: 6", while the mouse button is depressed. If you click and drag with the Ring tool, you can change the size of the ring you are drawing. Notice that the ring appears in Ball and Stick mode. We will change this to Line to match the style in the other document.
Hold the <Ctrl> key down while using the ring tool to make aromatic bonds directly.
Click and drag the Ring tool on one bond of the benzene ring so a 5-membered ring attaches to one side. Click and drag another 5-membered ring slightly away from the existing 5-membered ring. |
Throughout the rest of this lesson, we will refer to the atom labels on the luciferin molecule to help identify which of the atom locations we are referring to in our sketch (which does not yet have labels, bond orders, or atom types).
At this point in the lesson, we have reproduced the 2D geometry of the C1-S9 atoms and bonds as shown in our luciferin model in the right-hand document, and then atoms C10-S14, although we have not assigned the proper element types.
Saving your work
Let's save our work so far. We will name the molecule "MyLuciferin.msv".
Building chains
Now we will add the functional groups. Later on we will assign element types and add the double bonds.
Your sketch should now look something like this:
Alternatively, you can sketch the atoms as carbons, then select them and press the "O" key to change the element. Additionally, with the atoms selected, you can click the right mouse button for the Context Menu, and choose the Change Element... command.
Sketch the hydroxyl group onto the appropriate atom in the aromatic ring in the same manner as described above to complete the general framework of luciferin. |
At any point you can click the Clean command button to "clean up" the geometry of the molecule.
Adjusting bond order
Let's now sketch in the appropriate multiple bonds.
You can also select all of the bonds you want to change, and then click the appropriate bond order button on the Builder Toolbar.
Assigning elements
The final step is to change the element types. We need to change the atoms that will become the two nitrogen and two sulfur atoms, N7 and N11, and S9 and S14 in the original molecule.
Use the Select tool to select the atom that should be N7. <Shift>-click the atom that should be N11. While both atoms are selected, type N for nitrogen. |
Both atoms change to blue to indicate that they are now nitrogen atoms. There are a couple of other methods for changing atom types:
Alternately, you can modify element assignments by selecting the appropriate atoms and clicking the right mouse button to access the right-mouse pop-up menu. Then select S (for sulfur) from the Change Element list.
At this point, the atoms and bond orders in MyLuciferin should match those in the original luciferin model. The carbons should be gray, the nitrogens blue, the sulfurs yellow, and the oxygens red (if you have not altered the default color assignments).
Whenever you need to double-check this sort of result, you can turn on atom labeling (Label Object = Atom) and bond labeling (Label Object = Bond) to see each atom and bond's name.
Cleaning the structure
To complete our luciferin model, we need to clean up the 3D structure -- correct the bond lengths,
angles, and torsions. Additionally, we can add hydrogens. Although we could manually add each hydrogen, DS ViewerPro has an automatic function for this.
Make sure that the window with your sketch is still active, and use the Tools / Hydrogens/ Add command. |
Hydrogens atoms are added to the molecule. This same command can also be accessed
as the button on the
Builder toolbar.
Now we can clean the structure to see the final conformation and compare it to our original luciferin model.
Select the Modify / Clean Structure command
(or use the ![]() |
The Clean command standardizes all bond lengths, angles, and torsions according to the elements, bond orders, and hybridizations you have chosen. To examine this, use the various actions and display options you have learned in this lesson to look at the sketched model and the original model from several different angles by rotating the molecules.
Saving your work
If you haven't been doing so throughout the lesson, save your sketch now.
Studying your results
Here are some other things you can try while checking how closely your copy matches the original molecule.
Besides saving in standard molecular file formats and the Viewer's own format, you can save files as a graphic or a VRML file, email a file from within the DS ViewerPro application, or embed a "live" molecular graphic within an OLE-compliant program such as Microsoft Word, PowerPoint, or Excel.
To save as a GIF or JPG file (popular for web-based images), select the File / Save as command and choose the appropriate type in the Save as type list. Then you can use your web browser's Open command to view the file. Or you can display it in an HTML file.
The Quality setting (View / Options command) allows you to control the trade-off between higher quality 3D appearance and the speed of screen drawing. At the Low setting, you get fast drawing but less smooth details. At the High setting, you get a rounder, higher quality appearance, but making changes on the screen takes longer. When you are working with a model, work at the Low Quality setting, and then switch to High Quality before saving a graphic-format file.
2. Embedding molecular graphics.
Next we will embed a DS ViewerPro window in a Microsoft Word document. (You can choose another OLE-compliant application. The principle is the same.)
With nothing selected in the MyLuciferin document, select Edit / Copy. |
You need to start up an application to receive the copied molecule. We'll use Word.
Proceed through your usual start-up procedure for Word. |
Type a title for your document, and press return a couple of times. Select the Edit / Paste command. |
A small copy of the DS ViewerPro molecule appears.
Double-click in the graphic to activate the DS ViewerPro from within Word. This called in-place activation. |
The DS ViewerPro Menu bar and Tool palette appear in place of Word's.
The luciferin model in the embedded DS ViewerPro graphic responds. You can experiment further on your own with using the DS ViewerPro commands from within this document.
VRML output allows users who do not have the DS ViewerPro to see and manipulate a 3D image of your molecule through their Web browser.
Use the File / Save as... command and select VRML World Files (.wrl) as the Save as type. |
DS ViewerPro writes out a file that a VRML browser can read and display in 3D. For more information about VRML browsers, visit the web site at:
In this lesson we will study some of the display and labeling options that are especially useful for proteins.
The HIV Protease molecule used in this tutorial comes from the Protein Data Bank at http://www.rcsb.org/pdb/index.html. The MSV file provided results from reading the file 4hvp.pdb from the database into the DS ViewerPro and deleting the crystal waters for clarity.
Select the Open command on the File menu and select the Protease.msv file in the QuickStart folder. |
The molecule, HIV Protease, is displayed by default with the Line Display Style. You can choose the default styles applied when files are imported into the DS ViewerPro using the View / Options / Display Style page.
DS ViewerPro has several ways to display various aspects of protein structure. One useful thing to do when studying proteins is to turn off the atom display, so that the display is simpler, and quicker.
Clicking the Apply button makes the display modifications and leaves the dialog box open. Clicking the OK button applies the changes and closes the dialog box.
Let's look at some of the other display styles available for proteins.
If you'd like to see other perspectives of the protein with a particular display style, click the OK button and use the Rotate tool.
Protein-specific displays
The Solid Ribbon display shows folding of the backbone. The Hydrophobicity coloring shows the hydrophobicity of each residue colors the section of ribbon according to the hydrophobicity of the nearest residue. The deep blue colors are the most hydrophobic residues such as Leucine, Isoleucine, and Valine. The light blue residues are less hydrophobic residues such as PhenylAlanine and Alanine. The residues colored white are Glycines, and any residues unknown to the Viewer. The slightly red residues are slightly hydrophilic, and are exemplified by Proline, Tyrosine, and Tryptophan. The deep red residues are the most hydrophilic, and are residues such as Lysine, Glutamine, Arginine, and Glutamic Acid.
Open the Display Style dialog box again, and choose the Schematic display, and choose the Secondary Type color scheme. |
The Schematic display (Richardson diagram) details the location of helix and beta sheet regions.
Note that the 6-residue inhibitor in the HIV Protease active site is shown as a short segment of coil.
Use the Rotate tool to rotate the molecule until you can see that the beta sheet ribbon sections each have an arrow head at one end. This arrow points in the direction of the C-terminus. |
Investigating hydrogen bonding
This step shows how hydrogen bonds are involved in creating helices and beta sheets in the protein.
Open the Display Style dialog box, click on the Atom tab, and choose the Line Display Style and Color by Element. Click OK. |
The Viewer can show hydrogen bonds even when there are no explicit hydrogen atoms in the molecule. Of course, identifying hydrogen bonds without explicit hydrogen atoms is more of an approximation, and you might find that the number of hydrogen bonds differs when you add hydrogen atoms to the molecule.
Select the Tools / Monitors / HBond command. |
The green dashed lines indicate the hydrogen bonds.
The current display shows hydrogen bonds throughout HIV protease. If we wanted to see only the hydrogen bonds between the inhibitor and the protein, we could apply the HbondMonitor to the inhibitor alone. To do that, the inhibitor has already been defined as a Group.
With the inhibitor still selected, again choose the Tools / Monitors / HBond command. |
The display now shows hydrogen bonds between the inhibitor molecule, and the protein.
The hydrogen bonds displayed will change slightly because the algorithm is more accurate when the model contains explicit hydrogen atoms. We can now investigate how changing the orientation of the inhibitor in the active site changes the hydrogen bonding patterns.
With the inhibitor atoms still selected, choose the Rotate tool by pressing F6, or selecting it on the tool palette. Press the <Ctrl> key, and rotate the inhibitor in the active site. |
Hydrogen bonds break and form as you're rotating the inhibitor. See if you can find the orientation of the inhibitor that has seven hydrogen bonds.
Projecting properties onto surfaces
The Viewer can display a surface on a molecule. The surface can be colored by electrostatic potential, atom charge, parent color, or atom color.
Click on a empty part of the screen to ensure that nothing is selected and then click on the Fit to Screen button to bring everything into view. Select the Tools / Surfaces / Add command. |
A surface for the molecule is displayed, colored by electrostatic potential. The blue areas are due to positively charged atoms, and the red are due to negatively charged atoms. You can adjust several characteristics of the surface display.
Open the Display Style dialog box and click on the Surface tab. Turn on the Transparent option and click Apply. |
The surface becomes transparent but retains the same shape and coloring. You can see the Schematic protein display that was visible before we applied the surface. You can try the other options for surface display. Try rotating and translating the model while a surface is displayed. The various surface options are also interesting experiments when working with larger, more complex proteins or DNA.
Complex shows a protein dimer bound
to a yeast DNA fragment. This MSV file results from reading the pdb file 3cro.pdb,
then deleting crystal waters.
Customized display features for DNA: Yeast DNA and protein
In this lesson we will load a DNA-protein complex and take a look at some of the options that are especially designed for DNA viewing and analysis. We will use the file Complex.msv.
Use File / Open or one of the other open methods to load the Complex.msv file. |
You see a large number of atoms and bonds displayed using the Line Display Style. Changing the display styles for this model clarifies it quite a bit.
Now you can easily see the backbone of the DNA and the protein. You can further experiment with the combinations of DNA, Protein, and Atom Display Styles, if you like. The Rings Display Style represents nucleic acid chains as an arrow along the backbone pointing toward the C3' end, and sugar groups and bases as boxes. The Arrows Display Style (a subset of the Rings style) displays only the arrow along the backbone, pointing toward the C3' end.
Hierarchy window
Our next step in the lesson is to use the Hierarchy window to study the structure of these molecules.
Go to the Window menu and select New Hierarchy Window. |
The Hierarchy Window shows all objects that are in the molecular model, and their organization. The Viewer automatically opens the nodes to objects containing atoms, so objects that have a box with a [+] in front of the name contain atoms, or other objects. By default, bonds are not displayed in the Hierarchy Window. They can be displayed by clicking the right mouse button in the Hierarchy Window, and choosing the Display Bonds command.
The Hierarchy window shows that there are four amino acid chains in the 3D window, named D and E (DNA fragments), and A and B (protein dimer). Each chain or other "parent" object can be expanded to reveal its child objects by clicking on the [+] box next to the object's name. Clicking again collapses the object.
The Visibility tool allows you to selectively hide and display objects within the 3D window. We will investigate it briefly here, but you should take some time to try it on your own as well.
All of the objects in the 3D window are undisplayed, except for the object(s) selected with the Visibility tool. Each time you click a hierarchical object with the "magic wand", that object is the only thing displayed. The final action above causes all objects in the 3D window to be displayed.
You can use the Visibility tool to incrementally reveal the structure in a 3D window.
The display in the 3D window gradually builds, residue by residue, and chain by chain, from nothing to the complete set of structures.
Close the Hierarchy window and resize the 3D window and its molecule to your liking. |
The parent/child relationship comes in handy for expanding the set of objects affected by a selection. Double-clicking on a selected atom selects the parent of the selected atom(s), and all of the objects contained by that parent object.
In turn, you have selected one amino acid residue, that residue's whole chain, additionally selected a residue on the second chain, and then the entire set of two chains. The DNA chains remain deselected.
Pyrite is so common in the earth's crust that it
is found in almost every possible environment.
Display crystal structures: Pyrite
DS ViewerPro offers several visualization features that illuminate crystal structure. We will load a pyrite model to try out a few techniques. Pyrite is the classic "Fool's Gold".
Pyrite's crystal geometries are varied, and can include the cube, octahedron, a dodecahedron with pentagonal faces, plus crystals with combinations of these forms.
Open the PyriteCrystal.msv file in the QuickStart folder. To simplify window management, close any documents from the earlier lessons. |
First, use the Rotate tool to simply rotate and observe the model. Hold down the <Shift> key and drag the mouse around the window to rotate about the Z axis. |
This is an easy way to take a look at the connectivity of the lattices and the coordination of the atoms.
Using crystal display options
You now see a light gray lattice defining the repeat unit of the pyrite model, with the atoms represented in Line Display Style.The axes are labeled A, B, C, with an O for the origin.
The Lengths section of the Cell Parameters page tells the length of each cell axis, and the Angles section indicates that all the lattice angles are 90 degrees, consistent with this cubic crystal. On the Style page the options for Lattice Display (which we saw on the Cell Display Styles page) are repeated. We can experiment with the Space Groups settings:
Click the Space Groups tab of the Crystal Builder dialog box. |
The first scroll list shows the symmetry group number for this crystal. The Positions group lists the symmetry operators that are present in this model.
Click the Preferences tab. |
The Preferences page offers choices for Symmetry Style, Special Position Tolerance, Proximity Bonding, and View Range. You can use this last section to duplicate the crystal structure along each of the axes.
You now see only two atoms in each cell. The Positions setting reveals the actual non-replicate atoms in the unit cell. These are the minimal set of atoms that, when the symmetry operators are applied, generate the replicate atom positions through the crystal.
We could make this easier to see by selecting Replicate Atom in the Select dialog box (causing all the replicate atoms to be colored yellow in their selected condition). Or we could use the Tools / Labels /Add command to turn on labeling for the Atom Objects, which would only label the two non-replicate atoms. Particularly useful labels for the Replicate Atoms might be Name, ID, XYZ position, or (symmetry) Operator.
In the illustrated window, we see CPK style atoms in a Stick lattice. The Symmetry Style is Positions, and large green Name labels are applied to the Atoms while small blue Name labels are applied to the Replicate Atoms.
You have now completed the DS ViewerPro Quick Start lessons. There is more information about the individual features and how to use them in the online Help function within DS ViewerPro.
What you have learned
After completing these lessons, you have learned about: