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DS ViewerPro



3       Quick Start

This chapter gives you the opportunity to try some of the molecular visualization features in DS ViewerPro. While it doesn't discuss every feature, it does give you a good sampling of the types of things you can do with this program. After completing or just reading this chapter, you should be well prepared to experiment with the rest of the DS ViewerPro features.

This chapter discusses how to:

Import and display a small molecule: Luciferin
Sketch a simple molecule
Study a protein molecule: HIV Protease
Customized display features for DNA: Yeast DNA and protein
Display crystal structures: Pyrite

You will see the basic display, sketching, and file handling capabilities in the first two lessons, using a model of a luciferin molecule. The next lesson uses HIV Protease to demonstrate some of the commands that are provided for protein display and analysis.

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:

  1. Select the Save as... command on the File menu.
  2. Navigate to the folder where you want to save your modified DS ViewerPro document.
  3. This can be the QuickStart folder, where the original files are stored, or another folder of your choosing.

  4. Select the file type for your file. For these lessons, either save in the same format as the original molecule, or default to the Viewer file format (.msv).
  5. Type a filename for your molecular model file.
  6. 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.

  7. Once the above settings are correct, click the Save button.
  8. When you are ready to resume a Quick Start lesson, simply reload your molecule and continue from the point where you stopped.


Import and display a small molecule: Luciferin

Luciferin is the chemical that supplies a firefly's luminescence.

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

Start the DS ViewerPro program by double-clicking the DS ViewerPro program icon.

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.

Alternately
DS ViewerPro can be started several ways that simultaneously load the molecule of interest:

In Windows, you can also open the program from the Start menu on the Windows task bar.

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 luciferin molecule appears in a DS ViewerPro window. The default display style is Line. It is easier to see the effects of commands using one of the richer display modes, such as Stick or Ball and Stick.

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.

Select the Display Style button on the Toolbar: and change the Display Style to Stick. Leave the other options unchanged. Click OK. Make sure the pointer is in the luciferin document window. Click the Rotate tool: . Click and drag in the document window to rotate the view of the molecule. Try holding down the <Shift> key during a click-and-drag.

Next, try the other display effects on the Tool palette. Later, we will try the sketching tools.

Click each of the tools associated with the following actions and drag the pointer around inside the document window:
Translate Moves the molecule to different points in the plane of your computer's screen.
Zoom Dragging the cursor upward enlarges the molecule (zooms in); dragging the cursor downward decreases the molecule's visual size (zooms out).

Click the Torsion tool, then click on the central C-C bond and drag. Torsion Twists the orientation of the selected bond relative to the rest of the molecule.

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.

On the Toolbar, click the Fit to Screen tool: . Now click once in an empty area of the document window and select the View / Center command. Select the View/ Spin command. Select it again to turn Spin Off. Finally, select the View / Reset Rotation command.

You should observe the following series of results:

Fit to View: The document is resized to optimally fill the window with the selected luciferin.
Center: Both molecules move so the center of their center of geometry occupies the center.
Spin: Both molecules rotate until you toggle the Spin command to Off (no check mark in the menu).
Reset Rotation: The molecules return to the rotational view they occupied when they were loaded into the Viewer.


Sketch a simple molecule

In this section we will build a copy of the luciferin molecule and see how close it comes to the molecule we loaded earlier.

Preparing the document

We will be working with two documents -- one holding the loaded luciferin and one holding our sketch.

Click the Selection tool on the Tool palette and double-click on one of the luciferin copies to select the whole molecule. Use the <Delete> key (or the <Backspace> key) to remove one copy from the document.

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.

Use the Center and Fit to Screen commands (from the View menu) to position the luciferin molecule in the center of its window. Select View / Display Style to bring up the Display Style dialog box. Select Line for the Display Style. Click OK.

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.

Select the Tools / Labels... / Add command. The Object parameter should be set to Atom and the attribute parameter should be set to its default value of Name. If this is not the case, set them to these values and click OK.

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

Use the File / New command to create an empty document. Go to the Window menu and select Tile Vertical.

Your DS ViewerPro windows should appear similar to this:

Luciferin, and empty window

 

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.

Use the View / Options... command to open the Options dialog box. Click on the Sketch tab and set the Default Sketch Style to Line. Use the Selection tool to draw a bounding box around the 6-membered ring. When the whole ring is selected (a yellow highlight square appears at every bond and atom), use the Modify / Bond / Aromatic command to change the ring's bonds from single to aromatic. Click in the document window to deselect everything.

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".

Be sure the window in which you are sketching is still active, and select the Save as... command from the File menu. Select a file location and type MyLuciferin in the File name text box. The Save as type parameter should be set to Viewer (*.msv).

Building chains

Now we will add the functional groups. Later on we will assign element types and add the double bonds.

Click on the Sketch tool on the Tool palette to change to Sketching mode. Make a bond between the two 5-membered rings by clicking once on an atom of one 5-membered ring and then clicking on a (nearby) atom of the other 5-membered ring. (Atoms C8-C10 in luciferin.) Click on a carbon in the second 5-membered ring opposite to the bond you just made and move a little away and double-click (one click to create the bond, another to disconnect the rubber band) to add a carbon to the ring (Atom C20).

Your sketch should now look something like this:


We need to add the oxygen atoms of the carboxylic acid group, and the hydroxyl group on the aromatic ring to complete the basic framework of luciferin. The Viewer has a clever way to add carbonyl groups, or carboxylic acid groups. With the sketch tool, first click on the atom we added in the last step, the carbon atom in the carboxylic acid group. Sketch outward, and click to create the new atom. With the rubber band still attached to the cursor, sketch back to the original atom. Sketching over an existing bond increases the bond order, and in this case, makes the double bond. With the new atoms still selected, press the "O" key on the keyboard to change the atom to an oxygen. Then, sketch the second oxygen atom for the carboxylic acid in the same manner.

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.

At each bond in your sketch that should be a double bond (N7-C8; C10-N11; C20-O21 in luciferin), click once with the Sketch tool to change it to a double bond. (If you click on an incorrect bond or accidentally get a triple bond, use the Edit / Undo command. You can also adjust bond orders with the Modify / Bond commands.)

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:

Click and <Shift>-click to select the atoms that should be S9 and S14. Open the periodic table with the Modify / Element / Table command. Click on the element sulfur and then click OK, or double-click on sulfur to assign it to the selected atoms.

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 tool on the Builder toolbar).

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.

Select the Save command in the File menu. If you haven't already named the file, enter a filename such as MyLuciferin and set the Save as type to Viewer (*.msv) (or if it meets your needs, one of the other file types in the Save as type list).

Studying your results

Here are some other things you can try while checking how closely your copy matches the original molecule.

Exporting molecules

You can use the model you built in this lesson to experiment with the various export and interoperability features of DS ViewerPro.

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.

1.   Saving as a graphic file.

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.)

If necessary, start DS ViewerPro and load your MyLuciferin model. If you are continuing directly from the last section of this lesson, close the original luciferin document. If you are prompted to save changes, select No.

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.

You can rotate or translate the molecule to the orientation you want. Click on the Display Style tool. When the Display Style dialog box appears, select CPK (or another option of your choice) and click OK. You can also change the background color to match that in Word with View / Options / Graphics, and clicking on the color button.

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.

To return to Word control of the document, click in the Word document, outside the DS ViewerPro frame. When you are done with the Word document, close the Word file, saving it if you want to keep this example of an embedded molecule window.

3.   Creating a VRML file.

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:

http://www.web3d.org/vrml/vrml.htm


Study a protein molecule: HIV Protease

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.

Select the View / Display Style command to open the Display Style dialog box. Move the dialog box off to the side where it does not block your view of the model. In the Display Style dialog box, and on the Atom page, click Off. Click Apply, and the atoms disappear. Next, click on the Protein tab. The Protein page wasn't displayed in our previous exercises with luciferin because that molecule did not contain any protein information. ChooseSolid Ribbon and click OK.

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.

Open the Display Style dialog box again and choose the Protein tab if not already visible, and try various combinations of Display Style and Coloring combinations. Click the Apply button to see each display style in turn.

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

Open the Display Style dialog box again, and select Solid Ribbon Display Style and Color By Residue; click Apply. Try the pKa and Secondary Type Coloring options if you like. For the final settings, select Color by Hydrophobicity and click OK.

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.

Remove the HBondMonitor by selecting Tools / Monitors / Remove. Open the Edit / Select dialog box, click the Groups check box, and choose the Inhibitor group from the list. Click the Select button, and close the dialog box.

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.

Now, select the inhibitor atoms again, either using the Select dialog box, or clicking on one of the inhibitor atoms and then double-clicking twice to AminoAcidChain: I. Press the Fit to Screen button, or select View / Fit to Screen to zoom in on the inhibitor. With the inhibitor still selected, choose the Tools / Hydrogens / Add Polar Hs command to add hydrogen atoms to the polar atoms.

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.

When you are done experimenting with the surfaces use Save as... and rename your file if you want to save your view, or select File / Close and reply No to the prompt if you do not want to save your file.


Customized display features for DNA: Yeast DNA and protein

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.

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.

Open the Display Style dialog box and click on the DNA/RNA tab. Set the Backbone display style to Arrows and the Base Pairs display style to Ladder. Set the Coloring option to Color by Residue. Click Apply. Click the Protein tab and set the Display Style to Tube. Set the coloring to Secondary Type. Go to the Atom page and turn Off the Atom Display Style. Click OK to close the dialog box.

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.

Hierarchy Window with 3D Window

 

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.

Be sure the 3D window is active, then use the Display Style dialog box to set the Atom Display Style to Ball and Stick; Color by Residue. In the Hierarchy window, click with the Selection tool on the [+] box for C3'1 to expand the hierarchy to show the atoms within this amino acid chain. Click on the small structure icon next to C3'1 to select it and see the information reported in the Task bar pane: Nucleic Acid: C3'1. With C3'1 still selected, select Edit / Properties to get more information about this object.

Click on the Visibility tool ("magic wand" ) to change to the Visibility mode and click on the small structure icon next to C3'1. Click on various amino acids within the C3'1 amino acid. Then click on the O5 atom and <Shift>- click on the C6 atom. Try various combinations of selecting an object or a range of objects. Finally, click with the Visibility pointer in an empty area of the Hierarchy window to show all objects.

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.

Click the [-] box for the first residue, C3'1. Click the small icon with the Visibility tool and then <Shift>-click each object in turn down until all the residues in Chain D are displayed. <Shift>-click on the chain icon for Chain D to add the chain display. Then <Shift>-click on Chain E, Chain A, and Chain B.

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 the 3D window, choose the Selection tool and then click once on a spot on one of the protein (not DNA) chains. After this residue selection occurs (you can verify by checking the information in the task bar pane), double-click on the selected spot. Now, <Shift>-click a spot on the other protein chain and <Shift>-click in that spot again.

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.


Display crystal structures: Pyrite

Pyrite is so common in the earth's crust that it is found in almost every possible environment.

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

Open the Display Style dialog box and click the Cell tab. The Lattice Display is already set to Line. Click in the color box to open the Color Picker and pick a lighter gray. Click OK. Turn on the Label Axes option and click Apply in the Cell page of the Display Style dialog box.

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.

On the Atom page, change the Display Style to Ball and Stick. Change the Stick size to 0.1 Click OK. Rotate the model again. Open the Crystal Builder dialog box by selecting the Tools / Crystal Cell... command.

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.

On the Preferences page of the Crystal Builder dialog box, set the View Range for the A, B, and C axes each to 2. Click Apply. (You may want to close the Crystal Builder dialog box and use the Fit to Screen tool so you can see the entire lattice, then open the Crystal Builder dialog box again.) Then, on the Preferences page, set the Symmetry Style option to Positions and click Apply.

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.


What you have learned

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.

After completing these lessons, you have learned about:



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Last updated June 10, 2002.
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