29.1.6.5 Pop-up Menu Items for Peer

The right mouse button brings up a large menu of options for controlling peer. In the commands which specify how a molecule is drawn, the behavior of peer depends on whether any objects are selected. If no objects are selected, then all molecules are drawn in the specified way. However, if any objects are selected, then only the selected objects are drawn according to the command. For example, if you wanted to draw a transparent space filling view of a molecule on top of a vector drawing of the same molecule, you would do the following:

1. cat the peer input file twice and pipe it into peer.
2. Hit button 1, and select the Vector menu item.
3. Hit button 1 again to deselect the first object, and hit button 2. Select the space filling drawing type of your choice.
4. Select the Toggle object transparency menu item, and you are done.

The pop-up menu options are as follows:

Vector

Draw using vectors. If no objects are selected, then all molecules are drawn using vectors. If objects are selected, then only the selected objects are drawn using vectors.

Anti-aliasing

Toggles anti-aliasing for all vector drawn objects. Anti-aliasing greatly improves the appearance of vectors at a 50% performance penalty. This option does not work on Personal Irises.

Toggle depth cueing

Toggles depth cueing for all vector drawn objects. Depth cueing results in distant vectors being dimmer than close ones. This effect is not very pronounced for Irises in bright environments. This option does not work on Personal Irises.

12 sided polyhedron

Displays atoms as a regular dodecahedron. Object selection rules are the same as for Vector.

60 sided polyhedron

Displays each atom as 60 sided polyhedral sphere approximation. Object selection rules are the same as for Vector.

240 sided polyhedron

Displays each atom as a 240 sided polyhedral sphere approximation. Object select rules are the same as for Vector.

Sphere library sphere

Uses the Silicon Graphics sphere library for drawing spheres. The lowest resolution sphere is an icosahedron, and the higher resolution spheres are generated by dividing the triangular faces. The next menu item sets the resolution. This option can give the best quality spheres, but at a great penalty in performance.

Set sphere divisions

Sets the number of sphere divisions used for sphere library spheres. The text window where peer was invoked is popped to the foreground, and you are queries for your selection. If your response cannot be parsed as a number, then no change will be made.

Stereo

Toggles stereo display. In a stereo display, the screen is split in half, and left and right eye images are displayed. The stereo is "wall eye", so the left eye image is on the left.

Y rot +6

Rotates the view by six degrees. This option is essential for making stereo slides from the screen. To use it, simply take one picture, touch this item to rotate six degrees, and take the second member of the stereo pair.

Y rot -6

Rotates the view by six degrees in the direction opposite to the previous item. This is used to restore the view after a stereo shot is made.

Set Origin

Set the origin of rotation. The origin is set to the last atom picked using the left mouse button. When no molecules are selected, then the origin is for the entire picture. When molecules are selected, the origin for the rotation of the selected atoms. In this case, the picked atom must be in a selected molecule.

Reset object position

Reset positions. When no molecules are selected, the view is restored to its initial state. When molecules are selected, then each of the molecules is returned to its initial position. In order to do a complete reset of the picture to its starting point, start with no molecules selected. Then, touch this menu item. Then, select all molecules, and hit this menu item again.

Highlight objects

Normally, when objects are selected, they are displayed with a different color than normal. Alternatively, they can be displayed with their normal colors. This option toggles between those two possibilities.

Toggle object display

Toggles whether selected objects are displayed.

Color objects

This menu item will change the color used for selected objects. When touched, it will display another menu giving the choice of colors to use. Touch the color you desire, and all selected molecules will now have this color.

Color touched residue

This menu item will change the color of all the atoms in the residue of the last atom touched. When touched, it will display another menu giving the choice of colors to use. Touch the color you desire, and the residue will now have this color. Note: This color will be seen only when the molecule is not selected.

Reset residue color

This menu item will change the color of all the atoms in the residue of the last atom touched back to its initial value.

Color touch segment

This menu item will change the color of all the atoms in the segment of the last atom touched. It works analogously to Color touched residue.

Reset segment color

Reset the color of all the atoms in the segment of the last atom touched.

Define color

Allows you to define new colors. When this item is selected, the window where peer was invoked will be popped to the foreground, and the current color table will be displayed. You can then specify a new color as a name and three sets of low, high pairs of color intensities. The intensities must not exceed the range of 0.0 to 1.0, and the pairs are given in red, green, and blue order. Once you specify a new color, any commands which request color changes will show your new color as an option. If you make a mistake in the specification, then nothing will happen.

Toggle touched atom transparency

Toggles whether the last atom touched is displayed transparently.

Toggle touched residue transparency

Toggles whether the last residue touched in displayed transparently.

Toggle touched segment transparency

Toggles whether the last segment touched in displayed transparently.

Toggle object transparency

Toggles whether the currently selected objects are made transparent

Set transparency factor

Sets the transparency factor (alpha) for all transparent atoms. The window where peer was invoked is used.

Set background

Sets the background color. Currently, there is a problem with the interaction of transparent atoms with a non-black background, whose solution remains a mystery.

Change light direction

Change the direction of the light source. The coordinate system used for lighting has the x axis in the horizontal direction, the y axis in the vertical direction, and the z axis toward the viewer. The default direction is (0,0,1). The window where peer was invoked is used to type in this information.

Set shininess

Change the shininess of the spheres. This parameter is the same as the glossiness parameter (G) in the sphere drawing commands, see Sphere Lighting. The window where peer was invoked is used for this.

Write peer file

Ask for a file name, and write the current view to a new peer file. The new file presents the atoms in their current position, so molecule motions and views can be stored for later use, or for conversion to CONGEN format by peercg, see Peercg for more information.

Write CONGEN coordinates

Ask for a file name and a one line title, and write the current view to a new CONGEN file. The new file presents the atoms in their current position.

Remove Border

Turns off the border display. Note: This does not take affect until the window is completely redrawn, eg by a resize or an iconification. This option is useful for a full screen display.

Set draw frequency

This option is used to reduce the complexity of a drawing so that large objects can be moved more quickly. It specifies a reduction factor in the number of either atoms or bonds drawn. A value of 1 specifies everything should be drawn, and a value of n specifies that every nth atom or bond should be drawn. The value is taken from the window where peer was invoked.

exit

Exits the program. Nothing is saved by default.