THE 'STRATEGY' OPTION

INTRODUCTION

The 'Strategy' option assists the user with determining the best rotation ranges to be used to maximise the data coverage following an orientation determination (made using for example REFIX or DENZO) for a crystal. Results are presented for both a single contiguous rotation range and for two non-contiguous segments. There are also options to determine a series of up to five successive rotation ranges each optimised for data collection following the collection of the previous segments and to analyse for spatial overlaps.

List of sections:

Requesting the Strategy Option
The Strategy Method for Maximising Data Coverage
Examining the Results from Strategy Maximisations
Logging of the Results of Maximisations

REQUESTING THE STRATEGY OPTION

Introduction

When the 'Strategy' Option is selected, the following menu is displayed:

   <Maximise Unique Data>
   <Maximise Acentric Pairs>
   <Analyse Overlaps>

   <Return to Main Menu>

The first option is to determine a strategy which will maximise the unique data coverage and the second option is to determine a strategy to maximise the coverage of acentric data pairs. The third option enables an analysis of spatial overlaps for a series of oscillation angles so that a suitable oscillation angle may be selected for the data collection.

Note that the space group symmetry must be defined before the strategy calculation can be carried out. A check is made, where possible, that the crystal system and lattice type parameters are consistent with the space group information.

List of subsections in this section:

Maximising Unique Data or Acentric Pairs
Analysing Overlaps

Maximising Unique Data or Acentric Pairs

If one of the first two options is selected, a further menu is output in one of the the following two forms:

   <Current Set Only>
   <Current Set in Context>

   <Return to Main Menu>

or:

   <Current Set Only>
   <Current Set in Context>
   <In Context with MTZ>

   <Return to Main Menu>

The latter will only be output if there is currently MTZ data read in and stored in the program.

The strategy options parameter table enables the cell division factor to be cahnged if required. Also there is a toggle value to select whether or not 'Double Segment' stategy analyses are to be carried out. By default the value is 'yes' for maximising unique data and 'no' for maximising acentric pairs. In the latter case, the double segments option may well give poorer results because of the constraint imposed on the angle ranges examined; also the calculation is more time consuming than that required in the case of maximising unique data. The default values for the toggle are reset if the program defaults are reset or a new parameters file is read in.

In all cases, any values of the rotation ranges for the current crystal set are ignored as the purpose of the strategy option is to propose suitable values for these parameters. If the first option is selected, then the strategy calculation will be carried out for the current set alone. For the other cases, the strategy option determines rotation ranges for the current set assuming the data coverage from the other sets based on their currently defined parameters and, in the third case, also including any data read from an MTZ file.

Analysing Overlaps

If the 'Analyse Overlaps' option is selected, a further menu will be displayed as follows enabling either the selection of the rotation ranges as currently defined for the current set or input of a user selected range. The menu displayed is as follows:

   <Current Set Rotations>
   <Input Rotation Range>

   <Return to Previous Menu>

If the latter option is selected, input of a start and end angles for the rotation range is requested.

Having selected the required rotation range(s), the following menu is output to enable a choice of the oscillation angles to be examined:

   <Standard Oscillations>
   <User Selected Angles>

   <Return to Previous Menu>

If the first option is selected a series of five standard oscillation angles (0.5, 1.0, 1.5, 2.0, and 2.5 degrees) will be tried in sequence until 5% or more of the spots are found to be overlapped or until all five angles have been tried. If the second option is selected, the program prompts for up to five user selected oscillation angles. Input of a value of zero terminates the list.

After generating the unique reflections list and predicting the reflections covering the required ranges, a progress bar is displayed showing the progress of the spatial overlaps calculation for each of the selected oscillation angles. A cancel button enables the overlaps calculation to be interrupted if it is found to be too slow or if sufficient angles have been examined. As the analysis for each angle is completed, the results of the spatial overlaps analysis are output to a table in the main input output window giving the following items:

The oscillation angle
The oscillation scan range (total)
The estimated percentage of unique reflections recorded.
The estimated percentage of spatially separated unique reflections recorded.
The estimated percentage of spatially overlapped unique reflections recorded.
The estimated percentage of acentric pairs recorded.
The estimated percentage of spatially separated acentric pairs recorded.
The estimated percentage of spatially overlapped acentric pairs recorded.
The estimated percentage of spots which are spatially overlapped (fully or partially recorded spots).
The estimated percentage of the recorded unique data which are only present as spatially overlapped spots.
The estimated percentage of the recorded acentric pairs data which are only present as spatially overlapped spots.

The results are also written to the log file. The method used to estimate the overlaps is described in Appendix 5.

THE STRATEGY METHOD FOR MAXIMISING DATA COVERAGE

The strategy calculations are all based on 'quick' analyses of the data. A prediction is done for all reflections within the resolution range and their 'phi' values (rotation angles) are calculated. All reflections within a given phi range are assumed to be measurable unless they are within the cusp region or would not appear on the detector i.e. no distinction is made between fully recorded and partially recorded reflections and the oscillation angle is ignored.

The strategy option also makes use of the option to divide the cell by a factor to speed up the calculations very significantly though obviously with some loss of detail (see also description of quick analyses). The cell division factor for the strategy option and any subsequent quick analyses may be set via the parameter table under the menu area displayed when the strategy option has been selected.

Two basic strategy analyses are carried out by default. These are:

Single Rotation Analysis
For this option, the strategy calculation determines the data coverage for all possible rotation ranges in 5 degree steps an starting at all possible rotation angles again in 5 degree steps e.g. rotations of 5, 10, 15 ... 360 degrees starting from rotation angles 0, 5, 10, 15 ... 355 degrees. For each rotation range, the start angle which gives the maximum data coverage of the required type is found. The highest coverage for each rotation range and the corresponding rotation angle starting value is is presented in the results table (see 'Examining the Results') below.
Double Rotation Analysis
In some cases it is more efficient to collect the data in two separated rotation ranges and the double rotation range analysis determines the best two ranges to use. As the computations required are much greater than for the single range analysis, the calculations are carried out within a more restricted set of ranges. The program considers a first range size from 20 to 40 degrees (in 5 degree steps) followed by a gap of 20 to 40 degrees (in 5 degree steps) before the start of the second rotation range. Starting rotation angles from 0 to 90 degrees at 15 degree intervals and total rotations from 5 to 180 degrees in 5 degree steps are considered. For a short overall rotation range, the solution selected may be for a single rather than a double range. Also, because of the more restricted sampling ranges and start rotation angles, it is possible that in some cases, the data coverage from a proposed double range may be poorer than that found for the equivalent single rotation range.

When the results of the single and double range strategy analyses have been displayed, there is third option available which is to successively select a series of up to 5 rotation ranges. In this case each new segment is optimised as for the single rotation case and assuming the data coverage for the previous segments. It should be noted that with this option there is no overall optimisation of the multiple ranges. Thus for two rotation ranges this will, in general, give rather less data coverage that the double rotation analysis which optimizes for the combination of the two ranges.

EXAMINING THE RESULTS FROM STRATEGY MAXIMISATIONS

Introduction

When the requested strategy calculation has been completed a new strategy results window is displayed together with the following menu:

   <Quick Solution Analysis>
   <Full Solution Analysis>
   <Overlaps Analyses>
   <Choose Multiple Segments>
   <Accept a Solution>

   <Return to Previous Menu>

If multiple segments are selected, then the exact format of the menu will change; further details are given below. The basic options are to perform quick or full data coverage analyses on any of the solutions proposed by the strategy calculations, to make further strategy calculations based on a multi-segment analysis or to accept one of the solutions for use in data collection.

List of subsections in this section:

The Strategy Results Window
Choosing Multiple Segments
Analysing the Results
Accepting a Solution

The Strategy Results Window

The strategy results display window is divided into two sections, a text window displaying the actual results and an input/output window which is used for user input as needed. The strategy results table, at this stage, shows the results for both the single and (if the option is selected) the double range analyses.

Figure 1 Example of a Strategy Results Table

For each overall rotation range, the following items are output:

Osc: The overall ocsillation (rotation) range in degrees i.e. the single rotation range or the sum of the two ranges for a double segment.
Start: The start rotation angle for the single rotation range which gives the optimal data coverage.
%: The optimum percentage data coverage for the single rotation range.
%(2): If present, the optimum percentage data coverage for a two segment solution covering the same overall rotation range. Note that for the lower ranges, this may in fact also be just a single range.

The results for the first single and double ranges for which the data coverage is at least 90% are highlighted in blue. The results for the first single and double ranges for which the data coverage is at the maximum obtainable are highlighted in red. If both conditions occur for the same result, the highlighting in red is done.

If the mouse pointer is moved to the percentage coverage item, for a double rotation range, then the value will be marked by an underline and further details of the double rotation range will be displayed below the columns of results. The details show the sizes of the two rotation ranges and their corresponding start angles or, if a single range is optimum, the size of the rotation range and the start angles annotated with the message '- single range only'.

Choosing Multiple Segments

A series of up to five rotation ranges may be selected in sequence. First, the menu item <Choose Multiple Segments> is chosen. The program then waits for one of the solutions to be selected from the strategy results display window (the message 'Select first segment' is displayed in the active strip of the results text table). A solution is selected by using the mouse to point to the results for the required solution, when it will be highlighted, and clicking the left mouse button. Either a single range or a double range solution may be selected; in the latter case, this used as two segments in the multiple segments list. The current status of the multiple segments selection is then displayed underneath the other results. The <Choose Multiple Segments> option in the menu will be replaced by the two options:

   <Choose Another Segment>
   <Delete Multiple Segments>

The first new option alows another segment may then be added if desired. This involves a further single range strategy calculation and the display of a new set of results. A solution is selected from these results (the message 'Select segment' will appear in the active strip) and the program then re-displays the original results table with the multiple segments solution section being updated with the additional segment. The second option allows the multiple segments selection to be deleted, in which case the menu will return to its original form.

If another segment is selected then the <Delete Multiple Segments> option will be replaced by the option <Delete LAst Segment>. If the maximum of five allowed segements have been selected the <Choose Another Segment> menu item will no longer be present. Thus segments up to a maximum of five may be selected or segments from the end of the multiple segments list and finally the initial single or double rotation selection may be deletes as desired.

Analysing the Results

The results from any of the strategy solutions may be examined in detail using the Quick of Full analysis options or the Overlaps analysis option. These are basically the same as those described for the 'Analyse Data' option of the program.

When one of these options is selected from the menu, the user must then select one of the strategy solutions from results table (the message 'Select solution for analysis' will be displayed in the active strip). A solution is selected by using the mouse to point to the results for the required solution, when it will be highlighted, and clicking the left mouse button. Either a single range solution or a double range solution or the multiple range solution (if present) may be selected.

If a full analysis is requested, the required oscillation angle for an image needs to be input in response to a prompt in the I/O section of the results window of the form:

Oscillation angle [x.xx]:

The default value displayed is the current parameter value for the crystal set in question. The number of images to be measured and the overall rotation range, adjusted to be a multiple of the oscillation angle, are output.

It should be noted that if a quick analysis is requested, then no oscillation angle is assumed and the rotation range(s) resulting from the strategy calulation are used unmodified. On returning to the main menu and performing a quick analysis for the same rotation ranges, slightly different results may be obtained as, in that case, the rotation ranges are rounded up to be a multiple of the current oscillation angle.

If the 'Overlaps Analyses' option is selected, then, after selecting the solution to be analysed, the following menu is output:

   <Standard Oscillations>
   <User Selected Angles>

   <Return to Previous Menu>

If the first option is selected a series of 6 standard oscillation angles (0.5, 1.0, 1.5, 2.0, 2.5 and 3.0 degrees) will be tried. If the second option is selected, the program prompts for up to 6 user selected oscillation angles via the stretegy results input/output window. Input of a value of zero terminates the list.

After generating the unique reflections list and predicting the reflections covering the required ranges, a progress bar is displayed showing the progress of the spatial overlaps calculation for each of the selected oscillation angles. A cancel button enables the overlaps calculation to be interrupted if it is found to be too slow or if sufficient angles have been examined. As the analysis for each angle is completed, the results of the spatial overlaps analysis are output to a table in the strategy results input output window giving the following items depending on whether the maximisation is for unique data or acentric pairs data:

Unique Data

The oscillation angle
The oscillation scan range (total)
The estimated percentage of unique reflections recorded.
The estimated percentage of spatially separated unique reflections recorded.
The estimated percentage of spatially overlapped unique reflections recorded.
The estimated percentage of spots which are spatially overlapped (fully or partially recorded spots).
The estimated percentage of the recorded unique data which are only present as spatially overlapped spots.

Acentric Pairs Data

The oscillation angle
The oscillation scan range (total)
The estimated percentage of acentric pairs recorded.
The estimated percentage of spatially separated acentric pairs recorded.
The estimated percentage of spatially overlapped acentric pairs recorded.
The estimated percentage of spots which are spatially overlapped (fully or partially recorded spots).
The estimated percentage of the recorded acentric pairs data which are only present as spatially overlapped spots.

The results are also written to the log file. The method used to estimate the overlaps is described in Appendix 5.

Accepting a Solution

Normally one of the strategy solutions will be selected for use in the subsequent data collection. This is done by choosing the <Accept a Solution> menu item. The user must then select one of the strategy solutions from results table (the message 'Select solution to accept' will be displayed in the active strip). A solution is selected by using the mouse to point to the results for the required solution, when it will be highlighted, and clicking the left mouse button. Either a single range solution or a double range solution or the multiple range solution (if present) may be selected.

If no solution has been accepted when the <Return to Previous Menu> item is selected from the menu, a pop-up notice will be displayed and the user has the choice of returning in spite of not having accepted a solution or cancelling the return request.

LOGGING OF THE RESULTS OF MAXIMISATIONS

The strategy calculation results are written to the log file together with the results of any analyses carried out. The information presented is essentially the same as that described for the results window except that details are output of the rotation ranges and start angles for each of the double segment results. A note is made of any solution accepted.