THE 'ROTATION SIMULATIONS' OPTION

INTRODUCTION

This option allows for the display of Rotation simulations based on the current parameter values for the currently selected crystal set and image. When it is selected the following menu is displayed:

   <Colour Coded Display>
   <Interactive Display>
   <Interactive (x2) Display>

   <Return to Main Menu>

This allows for the selection of one of two modes of display, a colour mode and an interactive mode. In each mode there is a display area for the simulation, an area to list details of a selected reflection, a control panel area and an area used for requesting hard copy (Postscript) prints of the simulations.

'Colour' simulations show the rotation images with the spots colour coded in a number of different ways. 'Interactive' simulations are in black and white and have a slider which allows the user to investigate the effects of changing various parameters; spot labelling is also available. An interactive option may also be selected with the variable parameters used in the calculation set to twice their current value; in this case the current values for the variable parameters are used when the simulation is displayed and these may be either increased or decreased by selecting the required parameter and using the displayed slider.

Normally, by default, the rotation simulation view-object will be positioned just to the right of the main menu. It should be noted, however, that parameter table editing is active when rotation simulations are being displayed so that, if required, the rotation simulation display view-object may be moved to allow parameter values to be edited. When a parameter value is changed, the simulation will be recalculated and the new simulation displayed. In general the currently selected view-object options will be unchanged when the new simulation is displayed; however for 'Interactive' simulations it should be noted that if new values are given for any of the variable paramters,the lambda limits or then their new current values will be calculated based on the current slider positions; also, for 'Interactive' plots, all labels will be removed.

The variable parameters in interactive mode are as follows:

The rotation range for an image (in degrees)
The mosaicity in degrees (Eta)
The vertical beam divergence in degrees (Divv)
The horizontal beam divergence in degrees (Divh)
The wavelength dispersion delta-lambda/lambda times 1000 (Delamb)

List of sections:

Selection of the image
Orientation of the Simulations
The Colour Display
The Interactive Display

SELECTION OF THE IMAGE

The number of the image to be simulated is selected via the parameter table situated below the menu area when the Rotation Simulations option has been selected. When the Rotation Simulations option is selected, the initial value for the image number is set to 1. If there is more than one rotation range specified, then the image numbering for a range continues in sequence from that of the previous range. If no valid ranges have been defined, an error message is output when the display of a simulation is requested.

ORIENTATION OF THE SIMULATIONS

The simulations may be displayed in a number of different orientations. By default the orientation is the same as that from an IPDISP program display of a MAR image. An alternative program default may be set either via a command line option or an environment variable as described in chapter 1. The orientation options are 'ipdisp', 'denzo' or 'oscgen' indicating compatibility with programs of these names. When the Rotation Simulations option has been selected, the orientation appears as a parameter which may be changed in the parameter table situated below the menu area. If this value is changed then it will retain the new value until a new value is given, a new parameters file is read in or the program defaults are reset.

THE COLOUR DISPLAY

When this option is selected, the rotation simulation is displayed as coloured spots displayed on a black background. Various options may be selected via the control panel items. Also, details may be listed for selected spots and hard copy Postscript file plots produced if required.

Figure 1 Example of a Colour Rotation Simulation

Control Panel Options

The colour coding depends on the option selected via the Colour coding choice menu on the control panel. The display is qualified by the settings of other control panel items. The options available are:

Fulls/partials

The spots are split into three categories, fulls partials and those which are on the edge of the cusp region and are partly visible. They are colour coded as follows:

  blue:    fulls
  yellow:  partials (up to maximum used in the prediction)
  red:     cusp partials

Partiality 1

The spots are colour coded by their partiality as follows:

 blue:    fulls
 cyan:    partial <=n as set in the Partial 'n' panel item
 yellow:  partial >n and up to the maximum used in the
          prediction
 orange:  wide partial (greater than the maximum partiality
          used in the prediction)
 red:     cusp partial

Partiality 2

The spots are colour coded by their partiality as follows:

 blue:    fulls
 cyan:    partial =2
 green:   partial =3
 yellow:  partial >3 and up to the maximum used in the
          prediction
 orange:  wide partial (greater than the maximum partiality
          used in the prediction)
 red:     cusp partial

All the same

All the recorded spots are displayed in the same (blue) colour

Overlap status

The spots are colour coded by whether or not they are spatially overlapped. The colour coding is as follows:

 blue:    not overlapped
 yellow:  spatially overlapped spot

The 'Spot types' choice menu on the control panel allows the user to choose one of the following three options:

Display 'all' spots i.e. fulls and partials
Display fulls only
Display partials only

The display of spatially overlapped spots may be controlled via the 'Spatials' choice menu on the control panel. There are three options:

Display all spots including spatially overlapped spots
Exclude spatially overlapped spots
Display the spatially overlapped spots only

The user may select one of three spot sizes, small medium or large for the display via the 'Spot size' choice menu on the control panel.

The display, of a key at the top left of the display area showing the colour coding, may be turned on or off via the 'Key' choice menu on the control panel.

The partial 'n' value, used in deciding which category a partial spot is to be included in for the Partiality 1 colour coding option a nodal can be reset via the Partial 'n' value item on the control panel. The value must be in the range of 2 to the maximum value used in the prediction.

Listing Spot Details

When the mouse Button1 is pressed with the cursor on a spot position, details of that spot will be listed in the spot details area. The following information is listed:

The indices
The coordinates: The detector xd, yd coordinates in millimetres from the centre of the pattern.
The partiality: For a fully recorded spot the message 'fully recorded' is given. For a partial the partiality is given and the offset from the current image of the start image for the spot is indicated. 'Wide' or 'Cusp' partials are flagged as such.
The overlap status: The spot will be flagged asa 'non-overlapped' or as an 'overlapped' spot.

The selected spot is marked by a surrounding white circle on the display area. The selection may be removed by clicking Button2 or Button3 of the mouse (or Button1 when the cursor is within the display area but not pointing to a spot). When Button1 is pressed, the nearest spot to the cursor is selected provided that the distance squared (pixels) to the spot is no more than 18.

Hard Copy

To get a hard copy plot in the form of a Postcript file, select the panel button marked PS in the hard copy request area at the top of the view object. A question and answer sequence is then followed using a panel i/o item to the right of the PS button. Invalid replies will give pop-up error notices. The hard copy output may be abandoned by pressing the Escape key when a prompt is displayed. The question and answer sequence is as follows:

Postscript file name:: This reply is the name of the output Postscript file.
Spot diameter in mm [x.x]:: This gives the required spot size for the spots which need not be the same as that on the display. The default value given is an approximate match to that currently being used on the display. The reply must be in the range of 0.1 mm to 10.0 mm.
Add key [y]:: This enables the user to choose whether (the default) or not to display a key on the output plot. This key, with some additional information describing the nature of the plot, will be output below the actual rotation simulation.
Comment:: Up to 150 characters of comment may be input. The comment will be automatically split into lines if needed.

Note: On monochrome displays, these rotation simulations are of limited use as all the colours in the colour scales are represented by white. However any hard copy requested will have the normal colour representations in it.

THE INTERACTIVE DISPLAY

When one of the interactive display options is selected, the rotation simulation is displayed as black spots displayed on a white background. Various options may be selected via the control panel items. These include options to vary various parameters via a slider, options to highlight various classes of reflection and options to label selected reflections. Also, details may be listed for selected reflections and hard copy Postscript file plots produced if required.

Figure 2 Example of an Interactive Rotation Simulation

Control Panel Options

A 'Slider variable' panel choice item determines which of the available variable parameters can currently be adjusted via the slider. The parameters which may be varied under slider control are:

The rotation range for an image (in degrees)
The mosaicity in degrees (Eta)
The vertical beam divergence in degrees (Divv)
The horizontal beam divergence in degrees (Divh)
The wavelength dispersion delta-lambda/lambda times 1000 (Delamb)

The use of the slider was originally designed for use on colour displays which have 'writeable colour maps'. In fact 50 colours are used on the display with the spots being 'colour coded' by the value of the current variable parameter. The 50 colours are then set to white or black depending on the position of the currently selected slider. If the slider is moved then the display is altered merely by changing the colours in the colour map thus giving a rapid change of pattern as the slider is moved. On displays which do not have writeable colour maps and on monochrome displays, the use of the sliders is less effective as the pattern needs to be redrawn each time a slider is moved.

The current value for the parameter being varied is displayed to the right of the slider. The overall range is defined by the calling program.

The 'Highlight' choice menu on the control panel may be used to enable various classes of spots to be highlighted. The options available are as follows:

No highlighting: This is the default; all spots are shown as black spots.
Highlight fulls: Fully recorded spots are indicated by blue vertical crosses; partials remain as black spots. (on monochrome displays, the corresponding symbols are drawn in black)
Highlight partials: Partials with a partiality <= the value set via the Partial 'n' panel value item are displayed as blue vertical crosses; partials with a higher partiality are displayed as red crosses and cusp partials are displayed as green stars (or black on a monochrome display).

Note: When spots are highlighted and the soft limit sliders are used, the plot will be redrawn each time a slider is moved. The sliders are best used when no spots are highlighted.

The user may select one of three spot sizes, small medium or large for the display via the 'Symbols' choice menu on the control panel.

The partiality value defining the boundary between the two main classes of partials may be set via the Partial 'n' value item on the control panel. The value must be in the range of 2 to the maximum value used in the prediction.

The 'Labels' choice menu allows a number options for labelling. These are:

Labels off: No labels will be displayed and the labelling facility is currently disabled.
Labels on: Display any labels which have been added to the plot as described below.

If there are labels already displayed when a new labels option is selected, the existing labels will be redrawn as needed.

Note: When labels are displayed the plot may be redrawn if the slider is moved because a spot has disappeared or reappeared. The sliders are best used when no labels are displayed.

Listing Spot Details

When the mouse Button1 is pressed with the cursor on a spot position, details of that spot will be listed in the spot details area. The following information is listed:

The indices
The coordinates: The detector xd, yd coordinates in millimetres from the centre of the pattern.
The partiality: For a fully recorded spot the message 'fully recorded' is given. For a partial the partiality is given and the offset from the current image of the start image for the spot is indicated. 'Wide' or 'Cusp' partials are flagged as such.

The selected spot is marked by a surrounding red circle on the display area (black on a monochrome display). The selection may be removed by clicking Button1 when the cursor is within the display area but not pointing to a spot. When Button1 is pressed, the nearest spot to the cursor is selected provided that the distance squared (pixels) to the spot is no more than 18.

The spot details are also listed when a spot is labelled.

Labelling Spots

Providing that one of the labelling options has been selected via the 'Labels' choice menu, spots may be labelled on the plot as follows:

Move the cursor to the required spot.
Press and hold down Button2 of the mouse.
Move the mouse till the label is in the required position.
Release Button2 of the mouse.

A line is drawn from the nearest corner of the box surrounding the label to the labelled spot. When a label is being positioned, this line is shown while the label is near to the spot but if the label is moved far from the spot, then instead of the line, the spot position is marked with a large cross and the label is detached; when Button2 is released, the cross is removed and the attaching line is drawn.

Labels may moved as follows:

Move the cursor onto the label to be moved.
Press and hold down Button2 of the mouse. Note that when Button2 is pressed, the plot will be redrawn.
Move the mouse till the label is in the required position.
Release Button2 of the mouse.

Labels may be deleted as follows:

Move the cursor onto the label to be deleted.
Click Button3 of the mouse.

Hard Copy

Postscript file name:: This reply is the name of the output Postscript file.
Standard (s) or absolute (a) scale [s]:: With standard scaling, the simulation will be 18 cm square. For absolute scaling, the plot will be on the actual scale as determined by the crystal to detector distance. If this gives a plot larger than 18 cm square, then a warning message will be given and the plot will be clipped.
Spot diameter in mm [x.x]:: This gives the required spot size for the spots which need not be the same as that on the display. The default value given is an approximate match to that currently being used on the display. The reply must be in the range of 0.1 mm to 10.0 mm.
Symbol size in mm [x.x]:: This question is only asked if spots are being higlighted on the current plot. This gives the required size for the symbols to be drawn on the plot; these symbols need not be the same size as those on the display. The default value given is an approximate match to that currently being used on the display. The reply must be in the range of 0.5 mm to 10.0 mm.
Use coloured symbols [n]:: This question is only asked if spots are being higlighted on the current plot. By default the symbols on the hard copy will be plotted in black but coloured symbols may be requested if desired.
Comment:: Up to 150 characters of comment may be input. The comment will be automatically split into lines if needed.