Settings Menu (Startup Window)

Preferences - Sets parameters for modes of operation.

PostScript Settings - Hardware settings for direct PostScript output.

Pen Plotter Settings - Hardware settings for the pen plotter.

Palette - Modify, save or read the RGB values for the main 16-color palette.

Read Defaults - This reads structure display parameters, mostly those in the Input2 menu, from a setup file. These will replace those currently in memory.

Save Defaults - This saves structure display parameters, mostly those in the Input2 menu, for use when inputting a new structure with the New command in the File menu, or when a standard set of parameters is desired.

3.1.2.1 Preferences, Operation Tab

Dialog Box: Preferences - Operation Tab [ Settings Menu]

See also Preferences - Constants Tab.

Sounds. This turns on or off the sounds emitted by ATOMS, for example at the beginning and end of calculation and/or plotting (some system sounds are unaffected).

Draw into buffer. If this box is checked, the image is drawn into an off-screen memory buffer, and then copied to the screen. If not, the drawing is made directly to the screen, and then copied afterwards into the buffer. Drawing into a buffer is usually faster, but the difference may be small. No memory is saved by not checking the box, since the buffer is always used anyway for refreshing the window after another window is draw over it.

Confirmatory alerts in New input. If this box is checked, during input of a New structure file (File menu), after every input dialog there is an alert or dialog box (Entering New Data Set) giving the choice of proceeding to the next dialog, aborting data input, or revising the last dialog. Without these dialogs, there is no escape from the sequence of Input1 dialogs, and no escape from the sequence of Input2 dialogs.

Calculate query on file open. If this box is checked, you are asked if you want to calculate the structure - if not, the structure is calculated as soon as it is read in.

Scale lettering to screen. If this box is checked, in printed output or output to a file, the labels in that output will be scaled to approximately the same relation to the drawing itself as on the screen. This is a very approximate process, and trial-and-error adjustment will still be necessary to get the desired label sizes in output. This option should be thought of as adjusting the labels on the screen to look similar to those in the output, rather than the other way around.

Screen start-up. This sets the color/black-and-white state of the screen at start of ATOMS. It can be changed with the Color command in the Display menu.

Mark selected atoms. This refers to selecting atoms in the screen plot with the mouse.

If Show last is selected, the last atom selected is outlined in a contrasting color, but this marking disappears when another atom is selected, or an empty area is clicked. If Show all is selected, all markings remain until a Replot.

Skeletal mode during interactive rotation. When rotating using the mouse cursor, ATOMS can switch to a Skeletal mode so as not to slow down the motion. When

starting in 3D mode, the 3DSkeletal mode is used. This is not usually necessary when the number of atoms is small as the redraw is usually fast enough, so the best choice may be

"If more atoms than". The number of atoms may be 100 or so, but this will depend on the speed of your system.

Skeletal mode choice. Starting with V5.1 of ATOMS there are two possible methods of drawing in Skeletal mode. In the Bond colors or "old (pre V5.1)" mode, all atoms are shown as small dots, except those in polyhedra; all bonds are shown as lines using bond colors (either fill or edge colors as selected in the next item), and polyhedra are shown by lines joining the corners (outlining the faces). The lines indicating polyhedron edges use the polyhedron fill colors. In the Atom colors or "new" mode the bonds are shown in the

colors of the two atoms (fill color), half-and-half. Polyhedron edges are not shown;

instead the central-ligand bonds are shown.

Color for line bonds. When in the Skeletal drawing modes (Bond colors option above), and when bond radii are 0.0 in the Standard drawing mode, the colors for lines

representing bonds may be either the rim or fill colors given in the Bond Data dialog.

3.1.2.2 Preferences, Constants Tab

Dialog Box: Preferences - Constants Tab [ Settings Menu]

See also Preferences - Operation Tab.

Increment for drawing circles (degrees). Arcs of circles are drawn with line segments at specified angular increments (full circles are drawn with system routines). Ellipses are also drawn with proportionate line segments, although the increments are variable. The default circle increment of 12.0 degrees has been found to give satisfactory results for laser and pen-plotting, provided atoms are not too large. Making the increment smaller may improve the appearance, at a penalty in plotting time, especially if your computer has no math coprocessor or you are using lines of finite width.

On-screen rotation increment (degrees). This is the amount by which the image is rotated in the Dialog Bar - Left. This is the value which exists when ATOMS is started;

this value and not the latest value in the dialog bar itself is saved on quitting ATOMS.

On-screen displacement increment (Angstroms). This is the default amount by which a structure fragment is translated in the Dialog Bar - Fragments (Display menu). This is the value which is in the dialog when it is first called; this value and not the latest value in the dialog itself is saved on quitting ATOMS.

On-screen rescaling factor (%). This is the default amount by which the drawing is rescaled with the Scale button in the Dialog Bar - Right (Display menu). This is the value which is in the dialog when it is first called; this value and not the latest value in the dialog itself is saved on quitting ATOMS.

Default radius for atom location (Angstroms). When identifying atoms with the cursor, the given atomic radius is used for deciding when the mouse is clicked "on" an atom. However, if the input radius is zero or negative (denoting either polyhedral atoms or wire-frame atoms), this default radius is used instead.

Factor for scaling to screen or frame. In either the Maximize or Universal scaling modes (Scaling dialog, Input2 menu), the image is scaled to almost fill the screen or

frame. This factor specifies how close the image comes to the edges. This scaling is not precise when Perspective projection is used, so a relatively smaller factor may be

necessary if the perspective distance is small.

Dash length and dash ratio. The dashes are used for back edges of crystals

(Crystal Edges and Faces) and in display of Crystal Axes and Unit Cell. Length or repeat distance is in inches/centimeters, and the length factor is the actual length of the solid part divided by the repeat distance. Note that when using Frames in output the dash length remains the same - it may be desirable to decrease the length for very small plots.

Atomic radii. One or the other of the two files, ELEMENTS.ION,ionic radii, or ELEMENTS.COV, covalent radii, is used during input of Import files and input of atomic parameters through the Input Atoms dialog (see ELEMENTS files). The Factor multiplies the full radius values during this input. Values of around 0.5 are appropriate for ball-and-stick display, while values well over 1.0 may be required for interpenetration (space-filling).

Scaling units. This sets either inches or centimeters as the units for overall use in

ATOMS. This choice may be locally overridden for printing or other output by the Units setting in some of the dialogs involved.

3.1.2.3 PostScript Settings

Dialog Box: PostScript Settings [ Direct Postscript Output Dialog] [ Settings Menu] The page size, page margins and dots per inch/centimeter should be determined by the actual printer used for final output; if these are not correct, the drawing may not be scaled and/or placed on the page correctly.

The Transfer Function is analogous to the PostScript function of the same name. The linear option is standard; modify the function to get lighter or darker shading in

PostScript print-out.

Preview Color. If you select a screen preview (TIFF bitmap or PICT sub-file) in the Direct PostScript Output dialog, and if color output is selected, you can specify either a color or black-and-white bitmap. The Screen option uses the color depth of the the current screen display. Black-and-white PostScript output always uses a 1-bit or black-and-white screen preview.

Background color. If this option is on, the color selected in the Background Color dialog of the Input2 Menu will be applied in color output only. Background in b/w output is always white.

Atom algorithm. ATOMS shows shading for atoms by computing concentric zones around the point of emergence of the illumination vector. This can be done in two ways:

1) For non-PostScript display and output, points are calculated on lines radiating outward

from the point of emergence. This means that the curves defining atoms and atom shade zones are defined by a large number of short line segments - this is called the "lengthy"

algorithm. 2) The default algorithm for Postscript, called the "compact" algorithm, simply sends the parameters for the circle and ellipse segments which make up these curves (this cannot be done for normal drawing because the system drawing routines do not deal with general ellipses). The lengthy algorithm typically requires twice the disk space as the compact algorithm for shaded atoms. The compact algorithm is also more precise in its drawing of curves, and it allows all illumination vectors (for the lengthy algorithm, the point of emergence of the illumination vector must be within the atom outline, which may be truncated by interpenetrating atoms or large stick bonds). The only case in which the lengthy algorithm might be necessary is when three or more atoms interpenetrate, so that the segments removed from the outline of an atom overlap. This condition in principle could also arise if two stick bonds to an atom overlap.

Windows only

----If you are using direct output to a printer you must select the Port; this will be either

"LPTn" or "COMn". Also, if you are using a serial port for the printer, you must set or verify the data transmission parameters, such as baud, parity, etc., even if the port currently shown is the correct one. This is done in the Ports item of the Windows Control Panel (not in ATOMS).

3.1.2.4 PostScript Transfer Function

Dialog Box: PostScript Transfer Function [ Postscript Settings dialog]

The Transfer Function is analogous to the PostScript function of the same name. It changes the nominal gray values (0.0-1.0 for black-white) calculated by ATOMS as true illumination to values actually output. (Note that the PostScript gray scale, 0.0-1.0 for black to white, is in the opposite direction to the ATOMS gray scale, 0-15 for white-black; the transfer function applies to the Postscript gray scale.) If your printer gives gray shadings that are too dark (this is common, especially for lighter shades), you can

increase the output values. Values in between the listed values are linearly interpolated.

The actual gray values output to the printer or EPS file are changed; the transfer function itself is not part of the EPS file. Note that the gray-scale conversion also applies to lines of greater than single-dot width (single-dot lines are always black).

3.1.2.5 Pen Plotter Settings

Dialog Box: Pen Plotter Settings [ Pen Plot dialog] [ Settings Menu]

Current plotter radio buttons. There are several pre-programmed plotters; clicking on the Get Data button reads the pen-plotter data file (PPLOT) and obtains the commands and parameters. Even if your plotter is not listed here, you may be able to input the commands through the Other option. In this case, click on the Commands button to set

or revise the commands and parameters.

Pen-change mode radio buttons. If you have a multiple-pen plotter, you can elect to run in the Use single pen mode with the pen number entered in the edit field, and conversely if you have a single-pen plotter you can draw with multiple colors, but you will have to change the pens manually. If you choose the Change pens manually mode, the plotter returns to the zero position after drawing all lines of each color, and a message box appears, prompting you to change pens.

Blank border. A blank border can be added to atoms, bonds and polyhedra in the pen plot in order to increase the illusion of depth. Lines which are part of atoms, etc.,

"behind" the atom in question are cut off when they get within the specified distance of the atom, etc. which is in "front". This option may add considerably to the plotting time, since it involves much recalculation. If the width of the border is set to 0.0, there is no recalculation.

Speed number. This is the parameter (see Commands ) which controls velocity of the pen - for example for the Comrex, speed number 1 is slowest and 15 is fastest. Although some plotters, like the HP7475A, allow decimal speeds, you must use an integer here.

Windows only

----Port. This should be either a serial or parallel port: "COMn" or "LPTn". Even if this box shows the correct port, if it is a serial port you should verify the baud, parity, stop bits and data bits in the Ports item in the Windows Control Panel. These parameters should be set to match the settings on your pen plotter (which are usually controlled by DIP switches).

3.1.2.6 Pen-Plotter Commands and Parameters

Dialog Box: Pen-Plotter Commands and Parameters [ Pen Plotter Settings dialog] This allows you to enter or revise the pen-plotter commands and parameters, for non-standard pen-plotter types.

It is assumed that the plotter accepts ASCII commands that follow a simple syntax of

"command, parameters, terminator''. For example, the Hewlett-Packard command for moving the pen, raised, to the coordinates x,y is "PUx,y;''. "PU'' is the command, which should be entered (without parentheses) in the text box Move - pen up: x and y are the parameters, which are always supplied internally by ATOMS; and the semicolon is the terminator required in the Terminator text box. Commas between parameters are also supplied by ATOMS. Move - pen up means move to the new coordinates with the pen up (not marking).

You must enter or edit the commands in the text boxes on the left of the dialog. If more than one command is required to perform the operation requested, give all the commands with any intermediate parameters and terminators required, but omit the last terminator.

If your plotter does not use a command, just leave that field blank.

Following are comments on the plotter inputs. The type of variable required, and the maximum number of characters in case of a character variable, are given in parentheses.

View samples by clicking on the selections in the Current Plotter group in the Pen Plotter Settings dialog.

Commands

Move - pen up. (6 chrs) Move to the new coordinates with the pen up.

Move - pen down. (6 chrs) Move to the new coordinates with the pen down.

Raise pen. (6 chrs) Raise the pen without movement.

Pen speed. (6 chrs) This is the command which causes pen speed to be set or changed;

the parameter is entered as a separate item in the Pen Plotter dialog menu.

Change pen. (6 chrs) This is required only for multi-pen plotters.

Start plot. (12 chrs) Initialize the plotter. May require no commands, or several.

End plot. (12 chrs) Terminate plotting. Like (12).

Terminator. (2 chrs) The character which signals the end of a command. In most cases the semicolon.

Parameters

Maximum x/y. (Decimal) Maximum x and y coordinates. These values establish the centering of the plot. Increments on the x and y axes are assumed to be equal.

x/y at finish. (Decimal) The "base'' coordinates, in plotter units, to which the paper or pen will be returned at the end of the plot, or when pens are to be changed manually.

Units/inch(or centimeter). (Decimal) This establishes the resolution of the plotter and is used in scaling. If your plotter instructions do not give this number, divide the maximum x or y coordinate (item 1 above) by its length in inches.

3.1.2.7 Palette

Dialog Box: Palette [ Settings Menu]

The Palette is used to set up a 256-color palette for 8-bit screen display or raster output, and also to set the primary choices for color in all cases (you can always select other colors using different RGB values). See Colors, Palettes and Dot Patterns for more detail. The default Main palette has the same RGB values as the "alternate" palette used in DOS versions of ATOMS, but rearranged to a more logical order.

You can read and write values to palette (.PAL) files. Two palettes are provided on file:

STANDARD.PAL and ALTERNATE.PAL, which are respectively the standard IBM palette and the default alternate palette used in DOS versions of ATOMS. It is easy to write or modify the.PAL files directly; they simply contain the RGB values, from 0 to 255, separated by spaces (or commas).

The Default button will reset the palette to the current default values.

3.1.2.8 Read/Save Defaults

Read and Save Defaults Commands [ Settings Menu]

When inputting data for a drawing with the New command in the File menu (Startup) or File menu (Graphics), you can elect to use default values for display parameters, rather than set these in the dialogs of the Input2menu . If no data set is in memory, the default display parameters are always read from disk; and if there is a data set in memory, you can use the current values or read the defaults from disk.

Also, when importing a file (File menu (Startup) or File menu (Graphics)), you have the choice of reading in the saved parameters or using the current ones.

Also, if you desire to convert the current parameters, which may have been read in from a.STR data file, to the standard set, you can use the Read Defaults command at any time.

The Save Defaults option saves the current display parameters, i.e. most values in the dialogs of the Input2 Menu and some in the Display Menu.

Im Dokument ATOMS for Windows and Macintosh (Seite 37-44)