Keyboard Commands
Many Chem-Ray commands can be issued using the keyboard and the dialog box. Some of the commands are duplicates of menu or mouse actions, others are unique. There are a couple of secret keyboard commands. Don't tell anyone else and you will appear to be a total genius.
Atom Radius:
In the Chem-Ray element.tbl file each element is given a van der waals radius. When drawings are made in the ball and stick format, this van der Waals radius for each element is multiplied by the atom radius factor. Values of about .18-.25 are normal values. The atom radius command allows one to change this value.
ar program will respond with the current atom radius multiplier ar n specifies that the atom radius multiplier will be n
Bond Radius:
The bond radius command is used to specify the radius of the bonds in Angstroms in the actual pictures. A small value will give a skinny bond, a large value will give a fat bond. Strange things can happen if the bond radius is made larger than the atom radii.
br program will respond with the current bond radius
br n specifies that the bond radius will be n Angstroms.
Covalent Radius:
The purpose covalent radius command is to specify the covalent bonding radius of each element. The program will draw a bond between two atoms if the distance between them is less than the sum of their covalent bonding radii. Note that the element symbols are case sensitive. Co means cobalt, co is an unknown element!
cr Xx program will respond with the current bond radius for element Xx cr Xx n specifies that the bond radius for element Xx will be n Angstroms.
Exit
The Exit command closes all windows and exits the program. This is an absolute command. Use it with caution!
exit
Hydrogen bonds:
The hydrogen bond commands are used to specify various hydrogen bond parameters. The radius specifies the size of the hydrogen bond in the drawings. The distance represents the minimum H--acceptor distance needed to define a hydrogen bond. The default is 2.5 Angstroms. The angle is the minimum angle (donor-H--acceptor) needed to define a hydrogen bond, the default is 100 degree. Normally the program does not consider C-H hydrogen bonding. C-H hydrogen bonds can be turned on by the hb c command.
hbr program will respond with the current hydrogen bond radius hbr n specifies the current hydrogen bond radius in Angstroms
hbd program will respond with the current hydrogen bond distance hbd n specifies the current hydrogen bond distance in Angstroms
hba program will respond with the current hydrogen bond angle hba n specifies the current hydrogen bond angle in degrees hbc on turns on carbon as a hydrogen bond donor and acceptor hbc off turns off carbon as a hydrogen bond donor and acceptor
Labels:
The labels command simply turn on or off the atom labels. The labeling scheme must be specified using the menu command.
labels on turns on labels labels off turns off labels
Paging Commands:
The paging commands allow one keystroke paging through a .ctb file. These commands perform the same function as the upper right control buttons,
n display next molecule in list r reload current molecule p display previous molecule in list
Rotations:
Exact rotations around each of the three orthogonal axes can be specified using the following these commands.
x n rotates molecule around x axis by n degrees. n can be positive or negative. y n rotates molecule around y axis z n rotates molecule around z axis
Scale:
The scale command performs the same operation as the "ctrnl left mouse" operation, but it does so with an exact scaling value. Values larger than 1.0 make the molecule larger, values less than 1.0 make the molecule smaller.
sc n scales the molecule by a factor of n
Size:
The size command specifies the exact size of the molecular window in pixels. When the program first runs, the size of the molecular window is 350 x 350 pixels on most machines. The possible largest size of the window will depend upon the number of pixels available on your computer screen.
size n sets the molecular window to a size of n x n pixels
Stereo: A secret command
The stereo command rotates the molecule and the lights to generate the right hand image of a sterio pair. To generate a stereo image adjust the molecular view to give the desired image for the left hand member of the stereo pair. Copy the image into some other application using the clipboard. Then type the stereo command. The program will automatically rotate the molecule and the lights and redraw the image for the right eye using the same parameter set up. The default rotation is by a positive 5 degrees, other values including negative values for "crossed eye" images can be specified.
stereo draw the right hand image of a stereo pair after rotation by 5 degrees stereo n draw the right hand image of a stereo pair after rotation by n degrees
Styles:
The style command chooses the drawing style. Each style has an associated number. The style numbers are listed before the style on the pull down menus.
s n specifies style n chosen from the following list.
Available Styles
1. Lines 2. Sticks 3. Ball and Sticks 4. Charon 5. Chem-Ray Sticks 6. Chem-Ray Ball and Sticks 7. Chem-Ray Space Filling 8. Chem-Ray Sticks with Antialiasing 9. Chem-Ray Ball and Sticks with Antialiasing 10. Chem-Ray Space Filling with Antialiasing
Secret style Don't tell anyone
11. Poster mode. This is a secret experimental mode. It is sort of a bit map based Charon ball and stick drawing.
Translations:
The translation commands give exact control over molecular translations. They reproduce the "ctrnl right mouse" operation, but do so with an exact Angstrom value. They also allow z translations, something that is not possible with the mouse.
t x n translates by n Angstroms in the x direction. t y n translates by n Angstroms in the y direction t z n translates by n Angstroms in the z direction
van der Waals Radius:
The purpose of the van der Waals radius command is to specify the van der Waals radius of each element. The program uses thes value to determine what size to make the atom is any given drawing. In a space filling drawing the van der Waals radius of each element is first multiplied by the van der Waals multiplier, values of about .9 are typical. In ball and stick drawing the van der Waals radius of each atom is multiplied by the atom radius multiplier. Note that the element symbols are case sensitive. Co means cobalt, co is an unknown element!
vw program will respond with the value of the current van der Waals multiplier vw n specifies that the van der Waals multiplier will be n
vw Xx program will respond with the van der Waals bond radius for element Xx vw Xx n specifies that the van der Waals radius for element Xx will be n Angstroms.
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Last Update - July 27, 1997