OpenAstexViewer user interface

Mouse and Keyboard Controls

The view of the molecule that is loaded can be controlled using the mouse. The interface is similar (but not identical to) a number of other molecular graphics programs. In general only the left mouse button is used for controlling the view, as the right mouse button is reserved for bringing up the popup menu when OpenAstexViewer is running as an applet.

LeftMouse+Drag	Rotate the view of the molecule around the current centre point. This uses a straight forward 'virtual trackball' interface. Dragging near the top of the screen will cause a rotation around the z-axis.
Shift+LeftMouse+Drag	Scale the view of the molecule.
Ctrl+LeftMouse+Drag	Translate the centre of the view in the x,y plane.
Click on atom	Add that atom to the selection. If it is already selected, it is made unselected. When you click on an atom it is labelled and more info about it is displayed in the bottom left hand corner of the screen. Currently only one atom is labelled at a time.
Click on background	Clear the current atom selection
'+' key	Widen the clipping planes slightly, making more of the molecule available. [Note, this command is actually bound to '=' to avoid the user having to press Shift on a conventional keyboard].
'−' key	Narrow the clipping planes slightly, making less of the molecule available.
'c' key	Centre on the currently selected atoms i.e. to centre on a particular atom select it and then press 'c'.
'r' key	Reset the view back to the identity matrix, and recentre on all non-solvent atoms.
'd' key	If exactly two atoms are selected, the a distance monitor is added between the two atoms. This is a shortcut that avoid activating distance monitors from the menus (described later).
Ctrk + 'r' key	Select all the atoms in any residues that contain selected atoms. This is useful for centreing on a ligand. You pick an atom in it, press Ctrl+r (which selects all of its atoms) and then press 'c' to centre on those atoms.

Using the OpenAstexViewer Graphical User Interface

OpenAstexViewer version 2 has a more powerful graphical interface than the first version, which was principally intended for use as a preconfigured Applet running in a web page. The graphical user interface allows most operations to be carried out without the need for writing scripting language. This document provides a quick tour of the user interface, and then a few step-by-step guides for carrying out common operations.

Tour of the Menus

This section covers the menu bar at the top of the application. One of the options in the menu produces a control which has many more options and is covered later in the document.

File

This menu controls the loading and saving of molecules, maps and images.

Open structure...: This option provides a file dialog that lets you choose a molecule to load into OpenAstexViewer. Due to a limitation in the early versions of Java, the file choice is not restricted to valid molecule types. All files and directories are presented and you have to choose the PDB or mol file that you wish to load.
Open map...: This option provides a file dialog that lets you choose an electron density map to load into OpenAstexViewer. The same java feature means that all files are displayed in the file dialog. You may choose to load a CCP4 electron density map (with extension .map) or an Insight ASCII grid file.
Open object...: Load an OpenAstexViewer tmesh graphical object from a file.
Run script...: Run an OpenAstexViewer script. These should end with file extension .script. The scripts can carry out arbitrary sets of commands. As a convenience for developing scripts, the last script that was executed by "Run script..." can be re-executed by clicking in the graphics window and hitting the '!' key (reminiscent of the Unix '!!' feature which reruns the last command).
Save molecule: Pick a molecule from the pop up menu and save it. You can give it a different name, and change its type by providing a different extension. [Note, the file is saved in whatever file name you type, no extension is added by default]. If you overwrite the file file.pdb the previous copy of the file will be renamed file.pdb_00 (and so on) so that you still have a record of the old file.
Save view...: This option lets you write a script file that will recreate the scene as you have it now. This includes display styles, colors, graphical objects etc. It does this by writing a log of all the scripting commands since the session began. It should be possible to recreate a particular scene in OpenAstexViewer by either passing the script on the command line, or loading it via the 'Run script...' option. [Note, the absolute path of filenames are written into the file, which means that you cannot move the original file without editing the script to reflect the change. This is undesirable, and a later version will attempt to fix this by making the paths relative to where OpenAstexViewer is started].
Save all: This will overwrite all currently loaded molecules with their current coordinates. Backup versions of the files will be created as necessary.
Close: This lets you close a molecule and remove it from OpenAstexViewer. Any graphical objects that were derived from it will not disappear.
Write BMP...: This lets you save an image of the current view. Only windows bitmap files are supported, to maintain compatibility with Java version 1. It is possible that a future version will try and determine if the application is running with a newer version of Java which has support for different image formats. If the file name that is selected ends with '.gz' then the file will be written through a gzip compressor, which makes typical files about of the uncompressed size.
The menu choices let you choose the size of the image that you want to save. The 'Current size x?' options will preserve the aspect ratio properly. The other sizes just allow for the easy rendering of images that are larger than the window. It should be noted that all of the standard options perform 2x2 supersampling to provide some tantalising. On a PC with 256Mb of RAM you may not be able to write images that are much more than 2000x1500 pixels (4000x3000 before sampling). Rendering time is affected by size of image, image complexity, shadows etc.. You should not have antialiasing turned on in the image as this will cause an additional oversampling of the image.
Exit: Close the application. [Note, you are not prompted to save any molecules that have been changed. This is a bug, and will be fixed in the near future].

Select

The Select menu is almost obsolete apart from the options to bring up the Control Panel (described later) and the ability to quickly select ligands in the structure.

Popup...: Bring up the main control panel. This should appear at the right hand edge of the main graphics window. The controls are described in a separate section later in this document.
Clear: This option unselects all atoms that are currently selected (marked by a yellow dot). The same effect can be archived by clicking on the background of the graphics window.
Ligands: This will select all atoms that aren't part of the standard makeup of a protein structure (its as if the command 'select not (aminoacid or DNA or ions or solvent)' had been executed).
Ligand: This menu provides separate entries for each non-standard residue that appears to be a ligand. Its a useful way of selecting ligands, so that you can see them and centre on them using 'View > Center on Selection'.

Display

This menu controls the overall display of various entities within OpenAstexViewer. There are more sophisticated ways of achieving most of these actions in the control panel, but these are left here as they are occasionally useful as a shortcut.

Maps: Turn on or off the display of all maps. If maps are displayed then their contour levels can be controlled in the dialog obtained through 'View > Contour Levels'. When maps are turned off all contour levels are hidden.
Symmetry: Control whether or not symmetry atoms are generated when you recenter OpenAstexViewer. Their is a global spacegroup and unit cell which is determined from the first molecule that has symmetry defined. If CCP4 electron density maps are loaded then the symmetry information is taken from the first of these in preference.
Bumps: If bumps are selected then distance monitors are drawn between selected atoms and any neighbours that are closer than the sum of their vdW radii. The monitors are updated as you click on different atoms.
Solvent: Turn off atoms that are in standard PDB solvent residues.

Color

This menu changes the coloring of sets of atoms and the background of the main graphics window. All coloring options apply to the default selection. This is the currently selected atoms, or all atoms if nothing is selected.

By Atom: Change the colors of atoms back to the OpenAstexViewer defaults. Carbons are green (there is no way to change this default color - sorry all you people who like gray carbons), oxygens are red, nitrogens are blue, sulphurs are yellow, phosphorii are magenta, halogens are a variety of other colors.
By Chain: Colors each chain from a selection of different colors. See the scripting language documentation for the precise color details.
By B-factor: Colors each atom according to its b-value. See the scripting language documentation for the precise color details.
By B-factor Range: Colors each atom according to its b-value. The color scale covers the range from minimum to maximum b-value, rather than the predefined range used in the previous menu option. See the scripting language documentation for the precise color details.
Change to: Colors each atom with the color that was selected from the sub menu.
Background: Changes the background color to that chosen. The graphics are fogged to this color as well. To lessen the fogging effect you must move the back clipping further away. This can be done either with the '-' key or with the clipping plane tool in the control panel.

View

These command control certain aspects of the overall view of the graphics window.

Reset: Resets the orientation matrix to the identity matrix, and scales the viewport so that all the non-solvent atoms are visible.
Center On Selection: Adjusts the center point, width of the view and the clipping planes so that the current selected atoms are visible.
Clip Maps To Selection: Clip any displayed electron density maps to the region around any selected atoms. This is useful for tidying up electron density maps that are a little noisy.
Wide Bonds For Selection: Change the display style for the selected atoms to wide lines. This makes it easier to see the selected atoms. There are much more sophisticated display styles available in the control panel.
Contour Level Dialog...: Pops up a set of controls that let you change the contour levels for any maps that are loaded. Clicking the checkbox next to each contour level turns that contour level on or off. Clicking the label that displays the current contour level, will popup a color chooser that lets you change the color of the contour level. The slider lets the actual contour level value be changed.

Measure

Change the picking mode so that measurements can be made between sets of atoms. By default nothing is being measured, and picked atoms just get selected and labelled.

Distances: Each pair of atoms that is picked is joined by a distance monitor that shows the distance between those atoms. An alternative way to put distances in the view is to select exactly two atoms, and then press the 'd' key. This will create a distance monitor between the two atoms.
Angles: Each set of three atoms that is picked will get an angle monitor which displays the angle between the three atoms in degrees.
Torsions: Each set of four atoms that is picked will get a monitor which displays the torsion angle defined by the four atoms, in degrees.
Clear Distances: Clears all the distance monitors that are currently displayed.
Clear Angles: Clears all the angle monitors that are currently displayed.
Clear Torsions: Clears all the torsion angle monitors that are currently displayed.

Tour of the Control Panel

Select Tab

The main part of the graphical user interface is within the control panel. As described above, this is activated by choosing Popup... from the Select menu. The menu bar is at the top of the graphics window if OpenAstexViewer is running as an application or is available on a popup menu if running as an applet.

This section will talk through the control panel using the PDB structure 621p as an example. To load the structure you can either specify it as an argument to a command line script e.g.

OpenAstexViewer.bat r:\621p.pdb

or open it by File > Open Structure... from the menu bar. When you have loaded the structure get the control panel with Select > Popup.... At this stage the control panel should look something like the image below left.

The control panel has a number of tabs that allow the selection of sets of atoms, customisation of their display styles and the generation and modification of graphical objects.

The Select tab lets you choose sets of atoms, and apply display styles to them. The top half of the Select tab contains two sections that will select sets of atoms. Clicking on the symbol will expand the structure to show the protein chains that it contains. Chains whose identifier is the space character are labelled with an '_'. These can be expanded further to show the residues, and these can be expanded to show the atoms that the residue contains. The image above right shows what this would look like after expanding down to the N-terminal methionine in 621p.

Clicking on the name part of the structure browser (e.g. r:\621p.pdb or Chain _) will change the selection status of those atoms in the graphical display. The action is controlled by the three buttons at the top of the tab. If this is set to Select then all atoms in the item that is picked will be selected (i.e. a yellow dot will be drawn on them). If the mode is set to Append then the picked items atoms will be selected in addition to any atoms that are already selected (this lets you easily build up composite groups of atoms). If the mode is set to Exclude then the picked items atoms will be unselected, but all other atoms will be left alone.

To the right of the structure browser is another similar object, which is labelled Builtins. This contains sets of useful predefined selection statements that can be applied to many different structures. For instance, the Atoms group lets you select atoms according to their element. The Residues group contains all the common aminoacid residue names. Sphere lets you select groups of atoms that are within a certain distance of the currently selected atoms. Contact lets you select atoms whose sum of vdW radii are within a certain distance of one another.

The other groups let you select other useful subsets of atoms. The Whole residue feature will select all atoms in any residue that has at least one atom selected. The Whole molecule feature will select all atoms in a connected section that have at least one atom selected. The feature that is picked is affected by the selection mode at the top of the tab in the same way as picking atoms in the structure browser.

Sets of atoms can be picked from the graphical display as well. For instance, you might want to select the atoms in a ligand that you can see in the display. One way to do this would be to select a single atom in the display and then click on Whole Residue in the Builtins list. This should select the whole ligand residue (if it is all in one residue like in 621p.pdb).

Once you have built up a selection of atoms the controls in the Display as section can be used to change the display styles for the those atoms. The available display styles for atoms are Lines, Cylinders, Sticks and Spheres. Clicking the button next to a display style will turn that display style on for the selected atoms. Clicking the button next to a display style will turn that display style off for the selected atoms. The controls to the right of each display style will change the radii for the selected atoms.

Selected atoms can be lablleled using the label control. The menu provides a selection of useful labelling formats for the atoms. See the scripting language documentation for the meaning of the format expressions.

The final section at the bottom of the control panel is labelled View controls. This is visible in all tabs of the control panel. Hitting the Centre button will centre the view on the currently selected atoms. This does not change the rotation matrix. If no atoms are selected then the graphics display centres on all atoms. The Reset button will reset the view to centre on all non-solvent atoms, and will reset the rotation matrix to the identity matrix. The sliders labelled Front and Back let you adjust the position of the clipping planes. The numbers are distances in front and behind the centre point in Å's.

The final three buttons in this section control various graphical attributes. The Fog button should rarely be used as most objects will automatically depthcue/fog themselves into the background color (there is no way to stop this at the moment, but the degree of fog can be reduced by moving the Back clipping plane further back). The AA button will apply 2x2 supersampled antialiasing to the graphics display. The Shadows button will turn on simple shadow casting for the scene. This can be left on if desired but will considerably slow down rendering times (particularly if used in conjunction with the AA button).

Display Styles and Renderer Settings

This section shows some images that can be easily made for the ligand in 621p.pdb. With the structure loaded centre on the bound ligand. You can do this by picking an atom in it (the phosphate groups are quite obvious) and choosing the Whole residue feature from the Builtins table. Alternatively, expand the structure browser down to Chain _ and scroll through the list of residues to 167. Selecting this should highlight the ligand. You can now press the centre button to centre on the ligand. You will notice some gray lines near the ligand. This is automatically generated symmetry environment, you should probably turn this off by unchecking Display > Symmetry on the main graphics window menu.


Standard line display. Lines are drawn in width 2 for visibility.	Cylinder display. Note, cylinders are drawn analytically, not made of triangles.

Sticks display. Lines are drawn in width 2 for visibility.	Sphere display. Note, spheres are drawn as high quality bitmaps, not made of triangles.

Some Examples

This section gives step by step instructions for generating some more complicated images.

	Select `Aminoacid` from the builtins Choose `Color by B-factor` from the main color menu Choose `Spheres+` Select `Solvent` from the builtins Choose `Lines-` Select `Residue 167` Choose `Cylinders+` Check `Shadows` on
Protein displayed as spheres, colored by B-factor. Ligand displayed as cylinders, drawn with shadows.
	Centre on ligand as before Select `Atoms > Carbon` from the builtins Change `Color` to grey Select `Residue 167` Choose `Spheres+` Choose `Lines-` Choose `Transp 160` Select `Contact 0.5` from the builtins Choose `Cylinders+` Select `r:\621p.pdb` Choose `Lines-` Check `Shadows` on
Carbons colored grey. Protein within 0.5Å contact distance of ligand displayed as cylinders. Ligand displayed as transparent spheres, all with shadows.

Generate Tab

This tab contains controls for generating graphical objects. Graphical objects are constructed from atom positions, but after this are independent of them. For instance, they won't be turned off if the atoms that were used to generate them are turned off.

There are two principal types of graphical objects in OpenAstexViewer. These are molecular surfaces and protein cartoons (schematics). The controls for creating both of these types of objects are described in this section.

Molecular Surfaces

Molecular surfaces are created for the atoms that are selected in the graphics display. The surface algorithm is grid based and produces a triangulated surface. If you want to have more than one surface at the same time, you need to change the name of the surface in the Name: box.

The quality setting currently has no effect for molecular surfaces. They are always generated at the best resolution that can be made within certain limits of grid spacing and memory usage.

The Probe: control lets you specify the probe radius that is used for the molecular surface generation. The default is 1.5Å but some people prefer to use 1.4Å.

When you have the settings you want, press the build button and after a few seconds the molecular surface should appear. If it isn't quite what you wanted, modify the atom selection or the probe radius and regenerate the surface. As the surface name is the same as before it will overwrite the previous surface.

The surface is generated in white by default. The properties of the surface can be modified extensively using controls which are described in the Modify tab. These will be covered in detail in the next section.

Example Molecular Surfaces

Protein Cartoons

The main body of controls on the Generate tab is concerned with the production of protein cartoons (or schematics as they are sometimes known). OpenAstexViewer supports most of the common styles for schematic display.

The schematic generation acts on the currently selected atoms by default, or if nothing is selected it will work on all aminoacid residues in the currently loaded structures. The Name: box lets you specify the name of the graphical object that will be created. If you want more than one schematic object you must give them different names.

The Quality: spinbox lets you specify the overall quality of the schematic that is generated. It controls how many guide points are placed along the spline path, and the number of points around the perimeter of elliptical segments. Quality 1 has the least triangles and draws fastest. Higher numbers produce more triangles and somewhat better pictures.

The grid of controls beneath here control the shape and dimensions of the various different parts that are used to make up a protein schematic. Helices are drawn with a ribbon that follows the path of the Cα atoms. β-strands are drawn as arrows with an arrow head that shows the direction of the polypeptide chain. Other regions (coil) are drawn as a smoothed narrow tube that passes near the Cα coordinates.

The Oval checkbox determines whether or not helical ribbons are drawn as oval cross section ribbons. The cylinders checkbox controls whether or not cylinders are placed along the edge of a helical ribbon (this is not done if the ribbons are drawn with oval cross section). The cylinders look nice, but cannot be drawn transparently. If you think you want to make a schematic transparent then you should probably not use the cylinders option.

The Tube checkbox controls whether the schematic is drawn as all tube. These can be used for creating a solid Cα trace that looks as if it has been constructed from bent wire. You will probably want to adjust tube smoothing to 0 to ensure that the tube passes through the Cα positions.

The colors of the triangles that make up the protein schematic are taken from the Cα atoms at the time the schematic is created. A popular way of showing schematics is as a rainbow from blue at the N-terminus to red at the C-terminus. This shows the progression of the polypeptide chain. To achieve this, color the protein atoms by rainbow before generating the schematic.

The table below shows some of the protein schematics that can be generated for 621p.pdb. They also show the effects of varying some of the parameters, for each of the different secondary structure features.

Labels and Distances

The two final groups of controls in the generate tab allow you to specify sets of labels and distances for the structures.

The label controls will apply labelling to the currently selected atoms. You can control the string that they are labelled with bu choosing the an entry from the Value drop down menu. If you choose clear the labels are cleared for the selected atoms. The format codes are described in the scripting language documentation. You can put ordinary text in the label box as well. Characters preceeded by a \ will be drawn in Symbol font. The justify box lets you specify which part of the string will be used to justify the text. The XYZ buttons let you specify offsets on the screen after the text is transformed.

The 3d checkbox lets you choose whether or not you use a 3d font (which is constructed of cylinders). The button next to the Apply button will let you change the color of the labels.

There is currently no way to set the controls according to the current label style of a set of atoms. If you have labels with different settings you will need to recreate all the values for each set.

The distance controls let you specify sets of distances on the structure. The distance controls use sets of atoms that have been placed on the selection stack. To push a set of atoms onto the stack, you select what you want and then hit the Insert key on the keyboard. This will unselect the atoms. You can then push a second set of atoms onto the stack. The last set can be retrieved by hitting the Delete key. This pops the stack. Keep hitting Delete to clear the stack completely.

There are four different distance modes available on the top left menu of the distance controls.

Pairs: This variant uses two sets of atoms from the stack. It will generate a distance label between all pairs of atoms from set one and set two. The label is only added if the distance between the atoms is less than the value in Dmax and the distance minus the sum of the vdW radii is less than the value in Contact.
Nbpairs: This is similar Pairs except that the additional constraint that the atoms must be separated by at least 3 bonds is used.
Bumps: This mode uses only the top set of atoms from the atom stack. All pairs of atoms are considered for a distance monitor if they satisfy the Dmax, Contact and 3 bond rules.
Centroid: This mode uses two sets of atoms from the atom stack. The distance monitor is drawn between the cartesian center of the two sets of atoms.

The dash, gap and radius controls let you specify the size of the dashed lines that are used in the distance monitors. It should be noted that the dashes are drawn with a space of half the gap length at each end. The dash and gap values are adjusted slightly to achieve this effect. This stops large gaps appearing at one end or the other of the distance monitor.

The label controls how the monitor is labelled. The distance is substituted for any C language style floating point format. For example, the distance 3.456 would be shown as 3.4 if format was %.1f or 3.45 if format was %.2f.

The labels on the distance monitors are controlled by the current settings of the label controls. If you want to change how the label is formatted, change the label settings and then reapply the distances.

You can create multiple sets of distances by changing the name of the set. The only way to delete a set of distances is to clear the distance stack and recreate the distances.

The image above shows a custom distance label in OpenAstexViewer. It was created by selecting the atoms of the five membered guanine ring, and hitting the Insert key. Then the atom of the Phe ring was selected and the Insert key was pressed again. This means there are two sets of atoms on the selection stack.

Now, the settings for the font were changed to purple, 3d, size 0.5, radius 0.05 justification top left, and the distance label was changed to %.1f. This should give rise to a distance monitor like that shown.

Modifying Graphical Objects

The third tab in the control panel lets you change the attributes of graphical objects. Each object that you have created will appear as a separate entry. In the scrollable area of the Modify tab.

This is how the Modify tab would look if you had generated a molecular surface and protein schematic with their default names. Each object has its own entry and a number of controls.

From left to right across each entry the controls have the following actions.

The button marked with an 'X' will delete the graphical object.
The slider to the right of the delete button will vary the transparency of the object. Slider full to the right is completely opaque, with positions to the left being more transparent.
The black checkbox turns on the display of backfacing triangles. Backfacing triangles (i.e. facing away from the viewer) are usually turned off as they cannot be seen, and this helps rendering performance. However, if you have clipped into a surface or similar object you may want to turn on backfacing triangles so that it doesn't appear that the back of the object is missing. When the box is black backfacing triangles are not displayed. When checked it goes white, indicating that backfacing triangles are displayed.
The multicolored button to the right of the backface triangle control will bring up a color chooser control that lets you change the color of the object.
The Edit button brings up another control that lets you change calculate properties and apply texture maps for more sophisticated coloring schemes.
The final checkbox controls the display of the object. When the box is checked the object is displayed.

Editing Object Properties

The Edit button on the Modify tab will bring up a control that lets you generate properties for graphical objects as a function of atomic properties. These properties can be shown on graphical objects using texture mapping which is also controlled here.

The coordinate group lets you choose which texture coordinate you wish to calculate property values for. The u coordinate can be thought of as the x value of an index into an image, and the v coordinate as the y value of the index into an image. The u,v pairs are used to choose the color of the pixel according to the property value.

The properties section lets you choose which property to calculate for the texture coordinate. The properties are calculated using the atoms that are currently selected. The possibilities are

Electrostatic: Calculate a simple Coulomb electrostatic potential. The function uses a distance² dielectric constant. If the Charge checkbox is selected standard partial charges are applied to the aminoacid atoms prior to the electrostatic calculation. If you wish to supply your own charges these can be done with charge scripting commands, and you should uncheck the Charge box.
Lipophilicity: Calculate a simple lipophilic potential. The atom based contributions for aminoacids are automatically applied if the Contributions checkbox is selected. The contributions are stored in the charge attribute of atoms, so you can supply your own in a similar fashion to the electrostatic potential.
Distance: This will calculate the distance to the nearest selected atom and store that value at each point in the graphical object. The texture coordinates are normalised so that they become 1.0 at 8Å. If you have generated Distance texture coordinates for v then any pixels that lie outside the range are not drawn. This lets you generate very accurately clipped molecular surfaces, based on proximity to sets of atoms.
Curvature: This property estimates the curvature of an object using a smoothed function of the number of atoms within 8Å of the point on the graphical object. It is really only useful for molecular surfaces, and only makes sense when you generate the curvature using the same set of atoms that was used to generate the surface. It is a useful way of showing pockets in the binding site of a protein.
Atom colors: This function does not generate texture coordinates, but seems to make sense included in this part of the user interface. The function will map the color of the nearest atoms onto the molecular surface. The colors are blended to achieve a pleasing effect for molecular surfaces.
Clip: This also does not generate texture coordinates. Instead, it clips the object at the u or v = 1 line (depending on which coordinate you have selected). This removes triangles and vertices that lie outside this region. It will also accurately interpolate texture coordinates along triangle edges, and split them into subtriangles, to recreate the boundary. This can significantly speed up the rendering of objects that have large amount of triangles removed through texture clipping. It is particularly useful for permanently clipping parts of a molecular surface. This will make a partial surface cast better shadows [Note, once clipped, an object cannot be unclipped in this version].

Once, texture coordinates have been generated, you can apply a texture from the Textures. The origin of the texture coordinates is at bottom left, with u running to the right and v running upwards.

After calculating texture coordinates the minima and maxima of the property values will be shown in the spinboxes at the bottom of the control. You can change the values here to vary how the texture map is fitted to the calculated properties.

Examples of Texture Mapped Properties

Lights

The controls in the lights tab allow you to change the lighting model of the scene. To select a light, click on it on the circular control. It should turn yellow when it is selected, and the controls to the right will reflect its current settings. You can drag the light around on the circular control to reposition it. You can also slide the various intensity controls to change its strength and highlight contribution. OpenAstexViewer currently supports a global material type so all objects are illuminated using the current light settings.

The ambient control is for the whole scene, not for each light. Too much ambient light will make the shading very washed out.

The Cartoon button will switch to a lighting model that produces a simple cartoon style shading model. This only works well for spheres at the moment, but lets you produce simple color pictures like those of the Molecule of the Month pages at the RCSB web site.