THE 'ANALYSE DATA' OPTION

INTRODUCTION

List of sections:

Full Analyses
Quick Analyses
MTZ Data
Overlaps
Requesting the Analysis
Examining the Results

FULL ANALYSES

Full analyses make use of all the parameters which affect the prediction of spots on the rotation images. Such predictions are done on an image by image basis and the exact partiality of spots is determined. An analysis is also done for spatially overlapping spots.

QUICK ANALYSES

Full analyses may be quite time consuming especially for large cells and for many images. In many cases, a less detailed analysis may suffice and the quick analysis options in ROTGEN allow this to be done. Basically the program finds all the reflections within the required resolution limit and determines the rotation angles at which these would lie on the Ewald sphere. When analysing data over a given rotation range, all reflections with rotation angles within that range except for those occurring in the cusp region are considered to be acceptable provided that they would be recorded within the limits defined for the detector. No distinction is made between fully and partially recorded reflections. Also no analysis is done for spatially overlapped reflections.

The process is normally further speeded up by dividing each of the cell parameters by a factor of 2 (the default), 3 or 4 (this option may be set or turned off via the 'Quick Analysis Option' parameter table which is displayed when the 'Analysis Choice Menu' is present. This can increase the speed by a large factor but at the expense of decreasing accuracy of the analyses. Counts in the analyses tables are multiplied by the cell division factor cubed to compensate for the reduced cell size. If MTZ data are included in such analyses, then only MTZ reflections whose indices are all a multiple of the cell division factor are included.

It should be noted that the quick analyses options are only available when the beam and rotation axes are in the standard settings i.e. the X-ray beam along 'X' and the rotation axis along 'Z' (see Appendix 4).

MTZ DATA

Analyses may include MTZ data read into the program together with the full or quick analyses or on its own. Some care needs to be taken when interpreting analyses including such MTZ data as not all the information normally used in the analyses is present in the MTZ files (see chapter 4 and the sections below). When MTZ data is analysed on its own, the user may choose to use the resolution value from the MTZ file rather than that currently defined in the parameter table for the first crystal set.

OVERLAPS

This option allows for a more rapid and extensive analysis of spatially overlapped spots than can readily be achieved using the full analysis option. The analysis applies only to the current set. The same prediction algorithm is used as for the quick analyses though, of course, in this case the the full sized cell is used. The current set's oscillation angle is assumed. After generating the unique reflections list and predicting the reflections, a progress bar is displayed showing the progress of the spatial overlaps calculation. A cancel button enables the overlaps calculation to be interrupted if required.

On completion of the analysis, a results table gives 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.

REQUESTING THE ANALYSIS

When the 'Analyse Data' Option is selected, one of the following menus is displayed depending on whether or not there is any MTZ data currently stored:

   <Current Set - Quick>
   <All Sets - Quick>
   <All with MTZ - Quick>
   <Current Set - Full>
   <All Sets - Full>
   <All with MTZ - Full>
   <MTZ Data Only>
   <Current Set Overlaps>

   <Return to Main Menu>

   <Current Set - Quick>
   <All Sets - Quick>
   <Current Set - Full>
   <All Sets - Full>
   <Current Set Overlaps>

   <Return to Main Menu>

Note that the space group symmetry must be defined before the analysis 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.

When the analysis is initiated, the program first calculates a list of the unique reflections for the spacegroup and cell based on the resolution of the first crystal set defined. If the analysis for MTZ data only is requested then the following prompt will be output:

Use MTZ file resolution of x.xx (y/n) [y]:

For full analyses, the program outputs a message for each crystal set for which predictions are being done. If there is more than one image in the set, then, a progress bar will be displayed to indicate the progess of the predictions throughout the images of the set. A cancel button is also displayed in case the user wishes to abandon the analysis before it has been completed.

For quick analyses, the cell division factor should be set as required via parameter table 2 prior to selecting the required analysis option.

No further input is required for the spatial overlaps analysis.

EXAMINING THE RESULTS

Introduction

   <Show Reciprocal Lattice>
   <Show Graphical Plots>
   <Log Analyses w. Overlaps>

   <Return to Previous Menu>

Show Reciprocal Lattice
Show Graphical Plots
Log Analyses with Overlaps

Show Reciprocal Lattice

Figure 1 Example of 'Show Unique Coverage' View-object

The control panel contains the following panel items:-

• A drop down menu to select whether or not to include fully recorded reflections.

• A drop down menu to select which categories of partially recorded reflections are to be included in the plot.

• A drop down menu to select whether or not anomalous data is to be presented in merged or unmerged form.

• A drop down menu to select whether or not reflections predicted as being spatially overlapped are to be included in the plot.

• A button labelled 'DOWN' to move down one layer through the reciprocal lattice.

• A slider to select the layer of the reciprocal lattice to be displayed. If there are many layers, this may be used to get quickly to approximately the required part of the reciprocal lattice to be displayed. The 'UP' and 'DOWN' buttons may then be used to get to an exact layer if required.

• A button labelled 'UP' to move up one layer through the reciprocal lattice.

• A button to start or stop automatic cycling through the reciprocal lattice layers. This either has the label 'CYCLE' or 'STATIC' depending on the current mode.

• A slider to control the speed of automatic cycling through the sections.

The points on the unique part of the reciprocal lattice are marked by small greenish dots for those spots which have not been predicted/measured. Where anomalous data are merged, all predicted/measured reflections are represented by yellow dots. Where the anomalous data are to be separated the following colour coding is used.

       yellow:    Both an I+ and an I- reflection are present.
       red:       Only the I+ reflection is present.
       blue:      Only the I- reflection is present.
       white :    Unknown sign (i.e. both I+ and I- are not present
                  though I+ or I- may be present in addition to
                  measurements flagged as being of unknown sign.

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 control panel. 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.

Colour [y]:

The reply is 'y' (the default) if the colours are to be preserved in the postscript file. If the reply is 'n' then a black and white plot will be output. In the latter case, a dot indicates both I+ and I-, a + sign indicates I+, a - sign indicates I- and a diagonal cross indicates unknown sign.

Current (c), all (a), no. or range [c]:

There are four basic replies which may be made:

1. A reply of 'c' (the default) requests a plot of the current section only. The hard copy plot will be very similar to the displayed plot in this case.

2. A reply of 'a' to plot all sections; these will be output in a much reduced size form with nine plots per page of output.

3. The number of the section to be plotted (the section will be plotted as described for the current section plot).

4. Two numbers being the first and last sections to be plotted. These may optionally be followed by a third number being an increment in the sections to be plotted. The plots will be in the reduced size form with up to nine plots on a page.

Symbol scale factor [1.0]:

This will scale the default sizes used for the symbols by this factor. This may be used to improve the quality of the plot perhaps either to increase the symbol size for a small cell or decrease it for a large cell.

Comment:

Up to 150 characters of comment may be input. The comment will be automatically split into lines if needed.

Show Graphical Plots

   <Unique Data>
   <Acentric Pairs>
   <Multiplicity>
   <            >
   <Partials Toggle {<=nwmax]>
   <Overlaps Toggle [exclude]>

   <Return to Previous Menu>

   <Unique Data>
   <Acentric Pairs>
   <Multiplicity>

   <Return to Previous Menu>

• Partials with partiality <= nwmax (the default)
• None
• Partials with partiality = 2
• Partials with partiality <= 3

All the plots currently available are plots against resolution. The resolution range, from infinity to the resolution limit defined for the first crystal set (or from the MTZ file where relevant and where chosen), is divided into ten equal bins of 4.sin**2(theta)/lambda**2. The graphical plots which may be selected via the first three options are as follows:

1. Unique Data

   This plot shows the percentage of coverage of the unique data within each resolution bin. Where partials are included two lines are drawn, a blue one indicating the coverage for the full reflections plus the included partials and a red one indicating the coverage for the full reflections only. The overall percentage coverage for each of these cases is given at the top of the plot. Where no partials are included a blue line indicates the coverage by the fulls data and the overall coverage by the fulls data is given at the top of the plot. For quick analyses and for MTZ only analyses the latter plot is produced with all reflections being included in the counts.

   Figure 2 Example of a Unique Data Coverage Graph

2. Acentric Pairs

   This plot shows the percentage coverage of the unique acentric data within each resolution bin. A reflection must be present for each mate of a Bijvoet pair to be included. Where partials are included in the analysis two lines are drawn, a blue one indicating the coverage for the full reflections plus the included partials and a red one indicating the coverage for the full reflections only. The overall percentage coverage for each of these cases is given at the top of the plot. Where no partials are included a blue line indicates the coverage by the fulls data and the overall coverage by the fulls data is given at the top of the plot. For quick analyses and for MTZ only analyses the latter plot is produced with all reflections being included in the counts. Reflections of unknown sign from MTZ files are excluded from the analyses of acentric pairs.

3. Multiplicity

   This plot shows the average reflection measurement multiplicity within each resolution bin. Where partials are included in the analysis two lines are drawn, a blue one indicating the multiplicity for the full reflections plus the included partials and a red one indicating the coverage for the full reflections only. The overall average multiplicity for each of these cases is given at the top of the plot. Where no partials are included a blue line indicates the average multiplicity of the fulls data and the overall average multiplicity of the fulls data is given at the top of the plot. For quick analyses and for MTZ only analyses the latter plot is produced with all reflections being included in the counts. Reflections from a standard MTZ file will be included with a multiplicity of one or, if anomalous pairs are present, two and the analyses may thus not be a true reflection of actual situation.

Log Analyses with Overlaps