COSMO NT v1.40 User Manual

Transcription

1 %58.(5Ã$'9$1&('Ã;5$<Ã62/87,216 COSMO NT v1.40 User Manual Purpose These instructions cover use of the COSMO for Windows NT software package. COSMO is a software package for automated strategy determination for data collection. It includes an auxiliary for generating hardware description files. Responsibilities These procedures may be performed by trained Bruker AXS personnel and users. Disclaimer All configurations and specifications are subject to change without notice. 1 Introduction COSMO is an automated strategy determination program, designed to plan diffraction experiments on Bruker area detectors. COSMO lets you easily design an individual and appropriate data collection for every crystal and, thus, lets you obtain better data than a standard strategy would generally yield. On the basis of the orientation matrix and Laue group, COSMO automatically determines the best set of scans to collect subject to general criteria (such as the availability of time, desired redundancy, collision restrictions on the goniometer or low temperature device, etc.) that you may specify. 2 Fundamentals COSMO works with a large list of geometrically valid scans, the so-called basis set. This basis set usually consists of several thousand scans at different crystal-to-detector distances and goniometer/detector angles. The basis set is part of a hardware description file, which also contains the definition of rotation axes, detector(s), wavelength, etc. COSMO is shipped with a set of hardware description files (.hrd) for the standard Bruker diffractometers and area detectors. If necessary, you can generate individual files to take into account site-specific characteristic. This can be done with the help of COSMATIC, an auxiliary program that is part of the COSMO package. In order to determine a data-collection strategy, COSMO selects a suitable subset of scans from the basis set (determined by a user input resolution limit and crystal-to-detector distance), from which COSMO generates an optimum scan list based on a genetic refinement algorithm. The criteria used by COSMO for generating the scan list are completeness, redundancy, and total data-collection time. Each of the criteria has a user-input target and priority. The userinput priority tells COSMO how essential that particular target will be during the refinement process. The target value for the data set completeness is fixed to 100%. Finally, after the refinement of the strategy has finished, COSMO can be asked to sort the scan list to collect unique data first (as insurance against crystal decay). 3 Graphical User Interface COSMO is controlled by a Tcl/Tk based graphical user interface. Some parts of this interface make use of different colored text and graphics. A minimum screen depth of 16 bits (65536 colors) is recommended to avoid problems with the number of available colors. The following sections explain the menu items contained in the main window and the menu bar. A short tutorial at the end summarizes the steps of an ordinary strategy determination with COSMO in order to give an overview on how the different parts of the program work together. M86-E

2 Figure 1. Main window Main Window The main window is divided into a graphical and a statistical section (see figure above). The two graphs on the left side show the distribution of the data set completeness (blue) and redundancy (red) vs. resolution (top) and time (bottom). In the lower diagram, vertical lines (dark gray) indicate the transition from one run to the next. Also in the lower diagram, open boxes indicate the absence of at least 50% of the reflections of at least one unit cell axis. The exact value of each of the sample points in these graphs can be obtained by moving the mouse pointer to that position. A small label will appear containing the number corresponding to that sample point. The right side of the main window contains a table with statistical properties of the current data set and controls to change them (described in the next paragraph). Data Set Statistics This list on the right side of the main window summarizes the settings of various parameters of the currently simulated data collection and a statistical analysis of the data set that would result from it. The list is used to change these parameters and to define the target values for the data set completeness, redundancy, and total data collection time. For these three aforementioned target values, priorities can be set too. The list features the following items: Distance Crystal-to-detector distance (cm) Wavelength X-ray wavelength (angstroms) Mosaicity Crystal mosaicity (degrees) d High (best) resolution limit (angstroms) in resulting data set. 2 M86-E

3 2θ Diffraction angle (degrees) corresponding to the high resolution limit. sin(θ)/λ High (best) resolution limit (reciprocal angstroms) in resulting data set. Bijvoet Pairs Determines whether the Bijvoet (Friedel) pairs of reflections in reciprocal space will be merged prior to calculating the completeness and redundancy of the current data set, or not. If you are going to perform a MAD/MIR/SAS experiment or you want to determine the absolute structure of a chiral compound, the Bijvoet pair merging should be turned off. Laue Class Laue class of the crystal. Lattice Type Determines whether the systematic absences in the diffraction pattern of centered unit cells should be taken into account, or not. If a nonprimitive lattice is chosen, the systematically absent reflections are excluded from all further calculations. This leads to more precise data set statistics and, under certain circumstances, to an increase in program speed. If you specify one or more reflection files in the File > Import Collected Data dialog box, the lattice type must be set correctly. Otherwise, COSMO might not be able to predict a complete data set, or it might partially ignore data from the reflection files. a, b, c Unit cell axes (angstroms). α, β, γ Unit cell angles (degrees). Total Reflections Total number of reflections with different Miller indices. Unique Number of unique (independent) reflections (see Laue Class). Predicted Reflections Number of unique (independent) reflections generated from the current run list. Collected Number of unique (independent) reflections imported from a reflection file. Runs Number of runs. Frames Number of frames. Disk Space An estimation of the total disk space needed (in megabytes) to hold the whole data set. Completeness Data set completeness (percent). Redundancy Data set redundancy. Time Total data collection time (hours). Strategy Collection of preset target and priority value pairs for the data set completeness, redundancy, and total data collection time. These predefined values can be defined in the Edit > Preferences window. Menu Bar File Load/Save Configuration The current state of the program can be saved as a COSMO initialization file. These.ini files can be used later to restore all settings and continue the project. Initialization files named cosmo.ini are treated specially. On startup, COSMO checks to see if such a file exists in the current working directory and it reads the file s contents to restore the configuration automatically. You can also append the name of an existing initialization file to the command line prompt or drop the icon of an initialization file on the COSMO program icon to specify the project you are going to work on. Import Crystal Data Crystal and site-specific information (like the orientation matrix or the XY beam center) can be extracted from SMART.p4p, FRAMBO._pr, PROTEUM.spin, or DENZO.x files. Import Collected Data If previously collected and integrated data is available, you can enter the names of the corresponding reflection files in this dialog box. COSMO is able to read SAINT.raw, SHELXTL+.hkl, and SCALEPACK.sca formatted files. Export Strategy Writes a file containing the current strategy in standard Bruker run format. This run list can then be imported by SMART or FRAMBO. Exit Terminates the program. Edit Undo/Redo COSMO has extensive undo/redo capabilities, which allow you to take back or repeat the last 15 changes to almost any command executed from the graphical user interface. Custom Run List You can supply additional scans not contained in the basis set. This feature is to be used for that part of a data collection done in advance (in order to determine the crystal orientation matrix) and which is not reduced and integrated by the time COSMO is used. M86-E

4 Frame Width & Exposure Time Crystals differ in their diffraction power and mosaicity. The basis set used by COSMO to determine an appropriate data collection strategy is configured for a strongly diffracting crystal with a small mosaicity. This corresponds to a narrow frame width and short per-frame exposure times. This dialog box allows you to easily modify the frame width and exposure time of all runs contained in the basis set. Runs entered in the Custom Run List dialog are not affected. The exposure time is provided as a function of the diffraction angle 2θ vs. resolution. Use the Extend and Reduce buttons to increase or decrease the times for all seven sliders simultaneously. Click the Same button to set the six rightmost sliders to the same value as the first one. Figure 3. Figure 2. Preferences In the window that appears when you select this menu item, you can: add and remove hardware descriptions to and from the Hardware Profiles list and change the order in which the hardware descriptions appear in this list. add and remove scenarios to and from the Strategies list and change the order in which the strategies appear in this list. set the unit in which the resolution is shown in the data set completeness/redundancy vs. resolution diagram in the main window. You can choose between angstroms, degrees (2θ), and reciprocal angstroms (i.e., sin(θ)/λ). set the default run mode for runs taken from the basis set. View Use the Save button at the bottom of this window to save your current preferences so that they will be in effect each time you use COSMO. Note that the settings in the Frame Width & Exposure Time window will be saved with the four settings mentioned above. Detailed Strategy The window that appears when this menu item is invoked shows the contents of the current subset of scans derived from the basis set plus any runs you entered in the Custom Run List dialog. This list is intended to be used by the experienced user, as it provides detailed information and control over the strategy determination on a rather technical level. A typical list is shown: 4 M86-E

5 Figure 4. Each line in this list represents one scan determined by the crystal-to-detector distance, the angular positions of the goniometer and 2θ axes, the name of the scan axis, frame width, number of frames, and exposure time. In addition, every scan has a color code indicating its behavior during the strategy refinement. The following color codes are available for the scans: Black runs are "permanent" and always active during the refinement process and will not be altered by the genetic algorithm. This option is intended to be used for scans that have already been collected and, thus, definitely contribute to the final data set. Scans entered by the user in the Custom Run List dialog default to this color code. Red runs are considered as-is and can be deactivated throughout the refinement. However, if COSMO should decide to keep such a run active, it will remain in its original state (i.e., the angular positions of the axes and the scan range will not change). Blue runs are "partial" and can change their scan range during the course of the refinement. This option is the default setting for all runs taken from the basis set, because it offers the highest flexibility in fulfilling the desired data set completeness, redundancy, and total data collection time specified by the user. The default setting from runs taken from the basis set can be changed from partial to as-is in the Preferences window. Gray runs are "disabled," deactivated, and not taken into account at any time. To change the color code of a scan contained in the list: 1. Place COSMO in idle mode (i.e., the program must not be calculating the reflection list, refining a strategy, or sorting the scan list). 2. Select the run or runs you wish to change by pressing the left mouse button inside the scan list window or dragging the mouse while holding down the left mouse button. 3. Click the right mouse button inside the scan list to open a pop-up menu. Then select the desired color code (permanent, as-is, partial, or disabled). The scan list will then be updated and the contents of the main window recalculated. It is sometimes desired to change the color codes of all runs which lie inside a certain angular range of one of the axes or which have the same scan axis. In this case, click on the heading of the appropriate column to sort the scan list before applying the color code. Clicking the left mouse button on the heading will sort the scans in increasing order of the values appearing in the corresponding column, whereas clicking with the right mouse button sorts in decreasing order. Although the basis set contains a very large number of scans, you may want to use a run that is not contained in the basis set. (See also explanations for the Edit > Custom Run List menu command). If you specify additional scans in the Custom Run List dialog, COSMO will prefix the keyword Custom or Intern to M86-E

6 the appropriate scan to indicate the origin of that particular run. Reciprocal Lattice A projection of the reciprocal space is displayed on the screen. Dragging the mouse with the left mouse button held down freely rotates the image around the vertical and horizontal axes. Pressing the middle mouse button while moving the mouse up or down changes the zoom factor. On two-button mice, the left mouse button in combination with the Shift key can be used to emulate the middle mouse button. The image shows the three reciprocal space unit cell vectors (a*, b*, c*) corresponding to the Miller indices H, K, and L. The green transparent sphere in the center represents the volume of the reciprocal space that is covered by the currently set high resolution limit. Reflections that are missing from the currently simulated data set and are instead imported from a reflection file are shown in light blue. Reflections that are missing from the currently simulated data set but have a symmetry equivalent that was imported from a reflection file are shown in dark blue (the Equivalents check button at the bottom of the window must be turned on for this feature). The two sliders in the lower part of the window determine which reflections are displayed in terms of redundancy and frame number. Each slider has two handles. These handles are used to set a range from the lower to the higher redundancy/frame number. Vertical lines in the slider for the frame number mark transitions between runs. Hardware This menu contains a list of available hardware descriptions. You must select the correct item for the hardware on which the diffraction experiment will be carried out or, alternatively, you can supply your own hardware profile with the Custom Hardware Profile command of this submenu. If no configuration file has been supplied on program startup and if no cosmo.ini file exists in the current working directory, COSMO will automatically load the profile that was specified when COSMO was installed. Help Help Displays this online help text. About Shows information about this version of COSMO. Figure 5. Reflections are displayed as different colored boxes. The colors have the following meanings: Reflections that are collected by the runs of the currently simulated strategy are shown in light green. Reflections that are not collected by the runs of the currently simulated strategy but are instead covered by their symmetry equivalents are shown in dark green (the Equivalents check button at the bottom of the window must be turned on for this feature). Status Bar The status bar at the bottom of the main window contains a progress gauge, which is activated whenever COSMO is calculating the reflection list, refining the strategy, or sorting the scan list. All three processes can be interrupted be clicking the Stop button on the lower right side or, as an alternative, by pressing the Esc key. 6 M86-E

7 4 Start/Stop Refinement When the parameter setup is completed, you can start the refinement process by pressing the menu button at the lower right side of the main window (labeled Refine Strategy or Sort Runs for Completeness, depending on the action last performed by this button). Then choose Refine Strategy. The genetic algorithm will then modify the runs contained in the scan list according to their color codes and the target/priority values for the data set completeness, redundancy, and total data collection time. Under any of the following three conditions, COSMO will terminate the refinement process: You pressed the Stop button on the lower right side of the main window. The target values for the data set completeness, redundancy, and total data collection time have been reached. The refinement ended after the progress gauge reached 100%. 5 Sort Run List The scans contained in the resulting strategy can be sorted in a way that allows the fastest achievement of data set completeness. This is important in those cases where the particular crystal is known to be damaged by the X-ray beam and the available time should be used as profitably as possible. To sort the scan list in this way, press the menu button at the lower right side of the main window, then Sort Runs for Completeness. The Edit > Undo menu command can be used to restore the run list after the hemisphere runs generation. 7 Tutorial 1. Start COSMO and a new project. On starting a new project, COSMO has set default parameters and the default hardware description is loaded. 2. Choose File > Import Crystal Data and select either a SMART.p4p, a FRAMBO._pr, a PROTEUM.spin, or a DENZO.x file (depending on the software used for HKL indexing). 3. Set the correct Bijvoet pair merging, Laue class, and lattice type in the main window. If possible, COSMO will try to figure out the correct settings. However, in case of ambiguities, the program follows a defensive approach and selects the lower of the symmetries in question. Bijvoet pair merging is always assumed unless specified differently. 4. Specify the crystal mosaicity, the upper resolution limit, and the refinement target and priority values (the refinement strategy). The crystal-to-detector distance and the X-ray wavelength were automatically updated when the Import Crystal Data command was invoked (step 2) and correspond to your current hardware setup. At this time the data set statistics shows the maximal completeness that can be reached under the given circumstances, namely the crystal-to-detector distance, crystal orientation, and upper resolution limit. 6 Hemisphere Runs The most defensive approach for a data collection strategy in terms of completeness is a set of runs that will cover half of the sphere of diffraction. COSMO can complete such a list of runs when the Replace Strategy with Hemisphere Runs command is invoked from the menu button on the lower right side of the main window. All currently active runs in the strategy will be deactivated before the hemisphere runs are appended to the end of the list. Figure 6. M86-E

8 5. From the main window, press the menu button at the lower right side, then Refine Strategy to begin the strategy refinement process. The contents of the main window are now updated with every step of improvement COSMO makes. Note: If the refinement does not converge in the desired direction, interrupt the process by clicking the Stop button and go back to step 4. After the refinement has finished, the main window will look like this: Figure 8. If you are not satisfied with the results, undo the refinement by selecting Edit > Undo, and repeat the refinement with different parameters (step 4). 7. Choose File > Export Strategy to export the refined and sorted scan list. The resulting file can be read into the multi run editors of SMART and FRAMBO. Figure When the refinement process finishes, observe the result and perform the action that applies: If you are satisfied with the results, sort the scan list by pressing the menu button at the lower right side of the main window, then Sort Runs for Completeness from the main window. If COSMO is able to improve the run sequence, then the data set completeness/redundancy vs. time graph in the main window will change as shown: BRUKER AXS INC EAST CHERYL PARKWAY MADISON, WI USA TEL:+1 (800) 234-XRAY TEL:+1 (608) FAX: +1 (608) BRUKER AXS GMBH D KARLSRUHE GERMANY TEL: +49 (721) FAX: +49 (721) BRUKER NONIUS BV RÖNTGENWEG 1 PO BOX 811, 2600 AV DELFT THE NETHERLANDS TEL: (+31) FAX: (+31) info@nonius.nl Bruker AXS, Inc. All rights reserved. 8 M86-E