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THE 'ANALYSE DATA' OPTIONINTRODUCTIONThe 'Analyse Data' option enables the prediction of the reflections which would be recorded for the defined crystal sets and to analyse the data coverage in terms of the unique data for the space group, cell and resolution. The analysis may be done for either the current crystal set or for all crystal sets within the data set. The results may be presented in the form or histograms describing the data coverage or in terms of a pictorial representation of the reciprocal lattice sections. The analysis results equivalent to those displayed in the histograms are also written to the log file. The analyses automatically written to the log file exclude any spatially overlapped reflections.List of sections:
Full Analyses FULL ANALYSESFull 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 ANALYSESFull 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 DATAAnalyses 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.
OVERLAPSThis 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:
REQUESTING THE ANALYSISWhen 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>or <Current Set - Quick> <All Sets - Quick> <Current Set - Full> <All Sets - Full> <Current Set Overlaps>The current set is selected via the main parameter table. To perform the analysis the required item is selected depending on whether the predictions and analysis are to be done for the current crystal set only or for all crystal sets defined for the dataset as a whole and whether or not MTZ data are to be included in the analyses. No predictions will be done if only the MTZ data are analysed. 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]:If the MTZ file resolution is not used then the resolution defined for the first crystal set will be used instead. 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 RESULTSIntroductionExcept in the case of the overlaps analysis (where a results table is output to the main input/output window), the following menu is displayed when the requested analysis has been completed: <Show Reciprocal Lattice> <Show Graphical Plots> <Log Analyses w. Overlaps>The third option is only present after carrying out full analyses. The options enable the user to examine the results of the analysis.
List of subsections in this section:
Show Reciprocal Lattice Show Reciprocal LatticeThis option enables the presentation of the results in the form of a pictorial representation of the reciprocal lattice and the extent of coverage by the predicted data. A specially written XDL_VIEW object is used to display, in pictorial form, the coverage of the unique part of the reciprocal lattice by the currently predicted data. The main display area shows a single section of the reciprocal lattice at a time showing which reflections are part of the unique area of the reciprocal lattice and which of these reflections have been predicted or observed. Different categories of reflections e.g. fulls and/or partials may be included in the plot and, where appropriate, merged or unmerged anomalous data pairs may be indicated. Spots predicted as spatial overlaps may be included or excluded as desired but note that all data from quick analyses and from MTZ files is considered tp be non-overlapped. Spots which are classified as unknown full/partial (e.g. derived from an MTZ file of from a quick analysis) are included in the display as fully recorded (and non-spatially overlapped) spots. If anomalous separated data is displayed then these spots may also be of unknown sign (see below for colour coding). The user may change the section displayed using the 'Up' or 'Down' buttons or the slider provided. Alternatively there is an option to cycle automatically through the sections. In all cases the section axis is along 'l'. On the l=0 section the a* and b* axes are displayed. Two forms of hard-copy Postscript plots may be produced; one is basically a copy of the currently displayed plot and the other enables plots of all the reciprocal lattice layers (at a selected interval if required) in a more compact format with nine sections being output on each page.Figure 1 Example of 'Show Unique Coverage' View-object
The control panel contains the following panel items:-
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.The current layer number is shown both at the bottom left corner of the plot and to the right of the layer 'UP' button on the control panel. 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:
Show Graphical PlotsWhen this option is selected, one of the following menus is displayed depending on whether or not full analyses were carried out:<Unique Data> <Acentric Pairs> <Multiplicity> < > <Partials Toggle {<=nwmax]> <Overlaps Toggle [exclude]>or <Unique Data> <Acentric Pairs> <Multiplicity>The first three options enable different graphical analyses to be displayed. Then for full analyses and following a blank option there are two special options which are used to change the selection of which classes of reflection are to be included in the analyses. The 'Partials Toggle' selects which, if any, partial reflections are to be included in the analysis. The following choices are available:
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:
Log Analyses with OverlapsThis option is only available after full analyses have been carried out. The analyses automatically written to the log file exclude any spatially overlapped reflections. If the user also wishes to have analyses with the spatially overlapped reflections included, then the <Log Analyses w. Overlaps> option must be selected. A message indicates that the requested analyses have been written. If the option is selected again, before carrying out a new analysis, it will be ignored. |