Table of Contents
Summary of Contents for mar research Graphical User Interface mar345
- Page 1 Program Manual X−ray Research G.m.b.H. Segeberger Chaussee 34 D−22850 Norderstedt Germany research By Dr. Claudio Klein Tel.: (+49) (40) 529−884−0 Fax: (+49) (40) 529−884−20 Mail: info@marresearch.com Web: www.marresearch.com...
- Page 2 mar345 Program Manual ______________________________________________________________________________________ This document contains proprietary and confidential information of X−ray Research G.m.b.H.. The contents of this document may not be disclosed to third parties, copied or duplicated in any form, in whole or in part, without the prior written consent of X−ray Research G.m.b.H..
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Page 3: Table Of Contents
mar345 Program Manual ______________________________________________________________________________________ 1 Introduction 1.1 Computer Requirements 1.2 Environment 2 Running mar345 2.1 Command Line 2.2 Input Files 2.3 Output Files 2.4 Basic Concept and Rules 2.5 Starting Up 3 User Interface 3.1 Main Window 3.2 Menu Bar 3.3 Scanner Status Area 3.4 Scanner Command Area 3.5 Editing Data Collection Parameters... -
Page 4: Introduction
For a description of the setup of the mar345 software suite, see the "mar345 Installation Guide". IRIX 5.x, 6.x Compaq Tru Unix 4.x, 5.x RedHat 5.x, 6.x, SuSE 6.x Location of the scanner specific calibration files mar2300.XXX and mar3450.XXX and the corresponding configuration file config.XXX (where XXX = MAR_SCANNER_NO ). -
Page 5: Running Mar345
mar345 Program Manual ______________________________________________________________________________________ 2. Running mar345 2.1 Command Line The program mar345 should be started by just typing "mar345". The program, however, understands the following command line options: mar345 The command line options are: −h −colors N −def XXXX −host HOST −keep −more N... -
Page 6: Input Files
mar345 Program Manual ______________________________________________________________________________________ 2.2 Input Files The program mar345 requires the following input files to work properly: $MARLOGDIR/mar345.dat The program continuously saves edited parameters into this file. It is nice to find the program in the same state where you left it at startup. However, if mar345.dat cannot be found, program defaults will be used. -
Page 7: Basic Concept And Rules
mar345 Program Manual ______________________________________________________________________________________ The contents of the different types of log files are as follows: mar.log: mar.spy: mar.lp: 2.4 Basic Concepts and Rules The program has to perform different tasks: − Allow user input (i.e. change data collection parameters, analyze images, etc.) −... -
Page 8: Starting Up
mar345 Program Manual ______________________________________________________________________________________ 2.5 Starting Up Create a new window for running the program and type: "mar345". Do not run the program in the background and do not use this window for other purposes. The program will send important output to the window and you don’t want to miss it. At start up, the program will tell you something like: ============================================================= Program... -
Page 9: User Interface
mar345 Program Manual ______________________________________________________________________________________ 3. User Interface 3.1 Main Window Time until End of Data Set Current Time Progress Bar Shutter Status Collect Menu Scanner Command Area Menu Bar Scanner Status Area... -
Page 10: Menu Bar
mar345 Program Manual ______________________________________________________________________________________ The main window controls the most important scanner functions. It consists of different areas: − a menu bar − the scanner status area − the scanner command area 3.2 Menu Bar The menu bar features two buttons: Windows Pops up the Windows submenu (3.2.1). -
Page 11: Scanner Status Area
mar345 Program Manual ______________________________________________________________________________________ Move Distance Move Phi Reset Scanner Quit 3.3 Scanner Status Area The status area provides at all times all necessary information about the current status of the scanner.This part of the user interface changes dynamically according to the current scanner operation. -
Page 12: Scanner Command Area
mar345 Program Manual ______________________________________________________________________________________ Note: Timing is a crucial issue when operating the scanner. If the computer is very busy doing other computations, the internal clock of the program will work slower. A good check for excessive computer activity is if the X−windows server is not able to repaint the user interace at a reasonable speed. -
Page 13: Editing Data Collection Parameters
mar345 Program Manual ______________________________________________________________________________________ 3.5 Editing Data Collection Parameters... - Page 14 mar345 Program Manual ______________________________________________________________________________________ The Change Parameters window is used to program data collection parameters. The window comes in 4 slightly different flavours, depending on the button choice in the Collect Menu: − Single Data Set − Multiple Data Sets −...
- Page 15 mar345 Program Manual ______________________________________________________________________________________ Table continued from previous page. _______________________________________________________________________ Item ________________________________________________________________________ First image no. No. of images Exp. time Oscillations per image Starting Distance ________________________________________________________________________ For convenience, the program calculates the maximum resolution possible from the chosen distance and the chosen scan mode (image plate diameter). The image names are created according to the following convention: directory / root_TYPE_XXX.extension −...
- Page 16 mar345 Program Manual ______________________________________________________________________________________ In MAD Data mode "No. of images" is replaced by "No. of the number of images per contiguous images at a certain position and then the same wedge of data 180 degrees away. It is not such a good idea to collect only single images at one will have to move very often and that takes time.
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Page 17: Loading And Saving Data Collection Parameters
mar345 Program Manual ______________________________________________________________________________________ 3.6 Loading and Saving Data Collection Parameters Crystallographers often collect data of a certain crystal type in always the same way, i.e. using a certain oscillation range, a certain distance, etc.It is therefore useful to store a typical set of data collection parameters to a file and retrieve the parameters when desired. -
Page 18: Moving Distance And Phi
mar345 Program Manual ______________________________________________________________________________________ 3.7 Moving Distance and Phi The detector position and the mar345−Change Parameters window. One can also get separate windows for moving " " and "Distance" by pressing the corresponding status fields in the scanner status area of the main window and/or by activating the corresponding choices in the menubar of the main window. -
Page 19: Starting Data Collection
mar345 Program Manual ______________________________________________________________________________________ 3.8 Starting Data Collection Data collection can be started by pressing the "Go" or "Go/Erase first" button in the mar345−Change Parameters window. It is a good idea to always let the plate clean first before actually starting the data collection. In Multiple Data Sets mode, before actually sending the command to the scanner the mar345−Run Parameters window will pop up. -
Page 20: Single Scan
mar345 Program Manual ______________________________________________________________________________________ 3.10 Single Scan A single scan can be done by pressing the "Scan" button in the main window. The mar345−Scan window pops up. The directory, image root, image number and scan mode can be selected. The output format always is "mar345". Press "Scan" to start the scan A scan is always followed by an erase. -
Page 21: Getting Help
mar345 Program Manual ______________________________________________________________________________________ 3.12 Getting Help Interactive help can be obtained by pressing the "Help" button in the menu bar of the main window or by pressing the F5 key. In the mar345−Help window, a help topic should then be selected from the "Topics"... -
Page 22: Ray Setup
mar345 Program Manual ______________________________________________________________________________________ 3.14 X−ray Setup When producing images during data collection many parameters concerning the current experiment are automatically written into the output image headers, so this information can be retrieved later on. This is most relevant for parameters like the distance and the goniometer positions. -
Page 23: Errors And Warningsp
mar345 Program Manual ______________________________________________________________________________________ 3.15 Errors and Warnings During operation, i.e. data collection or other tasks, the scanner itself or the program mar345 might produce error messages or warnings. All relevant messages are displayed automatically in the mar345−Error window. This window can be popped up manually from the main window menubar or by pressing the F7 key. -
Page 24: Image Display
mar345 Program Manual ______________________________________________________________________________________ 4. Image Display 4.1 Display Window The image display window controls the most important display functions. It consists of different areas: Work area Information areas Menu bar Window title Image area... -
Page 25: Menu Bar
mar345 Program Manual ______________________________________________________________________________________ 4.2 Menu Bar The menu bar features the following buttons: Windows Pops up the Windows submenu (see 4.2.1). Shortcut: Alt+w. Options Pops up the Options submenu (see 4.2.2). Shortcut: Alt+o. Help Pops up the mar345−Help window. 4.2.1 Windows Submenu The Windows submenu pops up when the "Windows"... - Page 26 mar345 Program Manual ______________________________________________________________________________________ Do not/Keep color scales Reset colors Turn On/Off 3D−plot Next image Previous image Integrate Zoom options Normally, if a new image is loaded, the program recalculates a new color scheme. If you want all images to be displayed in the same way, select "Keep color scales"...
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Page 27: Image Area
mar345 Program Manual ______________________________________________________________________________________ 4.3 Image Area In this area, the image is displayed. With the pointer (3−way mouse button) several additional functions can be accessed. ________________________________________________________________________ Button Action ________________________________________________________________________ Left Press Drag Release ________________________________________________________________________ Center Press ________________________________________________________________________ The right mouse button functions depend on the current zoom factor. At zoom factors < 1, the behaviour is as follows: ________________________________________________________________________ Button... - Page 28 mar345 Program Manual ______________________________________________________________________________________ At zoom factors > 4 one can obtain a 3−dimensional representation of the magnified portion of the image. For this feature, use "Turn On 3D−plot" in the Options menu of view window or toggle this option by pressing Ctrl+d. In 3D mode one can still move around within the image by pressing the right hand mouse button, but the recentering corresponds to the position of the 2D display, so this time it is more guessing.
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Page 29: Workr Area
mar345 Program Manual ______________________________________________________________________________________ 4.4 Work Area 4.4.1 Load Buttons By pressing the single left or right arrow one can decrease or increase the current image number and load the previous or next image, respectively. The double arrow will continously increase image numbers and continuously load the next image until the stop button is pressed. -
Page 30: Window Title
mar345 Program Manual ______________________________________________________________________________________ 4.6 Window Title In this area, the image name and some parameters extracted from the image header (total number of pixels along x, number of pixels with intensities larger than 65535) are displayed. 4.7 Colors Window In this window, colors may be modified. - Page 31 mar345 Program Manual ______________________________________________________________________________________ The functions of the mar345−Colors window widgets are: Grey scales Selection of coloring mode. Alternatives: Blue scales, Rainbow. All pixels with intensities <= Min are drawn white (black in Blue scales). The dashed line in the histogram plot moves to the specified value. All pixels with intensities >= Max are drawn black (Grey scales), white (Blue scales) or red (Rainbow).
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Page 32: Cross−Section Window
mar345 Program Manual ______________________________________________________________________________________ 4.8 Cross−Section Window This window is used for displaying cross sections through the image. The window can be obtained by pressing the left mouse button in the image area. The functions for the mar345−Cross section window widgets are as follows: No. - Page 33 mar345 Program Manual ______________________________________________________________________________________ The plot area of the window shows the following features: Vertical axis Upper horizontal axis Lower horizontal axis Left dashed red line Right dashed red line Horizontal red lines The pointer can be used to measure distances by setting the red dashed lines to the desired position along the drawn line.
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Page 34: Data Collection
mar345 Program Manual ______________________________________________________________________________________ 5. Data Collection 5.1 Strategies While some general rules apply how to collect data best, a sensible choice of data collection parameters depends on individual circumstances, i.e. crystal quality, beam properties, etc. The following section gives some hints on how to program a data collection: Distance crystal−detector: The distance crystal−detector must be chosen such that spots don’t overlap. -
Page 35: Checking Parameters
mar345 Program Manual ______________________________________________________________________________________ The decision about what pixelsize to choose is slightly more difficult. In general, the finest pixelsize of 0.1mm is more efficient and yields slightly better data. On the other hand, scans take about 10% longer time and images are larger in size than those taken at the same diameter but in 0.15mm pixelsize mode. -
Page 36: Troubleshooting
mar345 Program Manual ______________________________________________________________________________________ 6. Troubleshooting Both the computer and the scanner can produce fatal errors and warnings. All messages are numbered. Messages with message numbers < 1000 come directly from the scanner controller and are potentially serious. Message numbers >= 1000 are generated by program mar345 and may be a consequence of a controller error or some other kind of malfunctioning or warning. - Page 37 mar345 Program Manual ______________________________________________________________________________________ Tabel continued from previous page. _______________________________________________________________________ Description _______________________________________________________________________ 1050 Message: Reason: Action: 1060 Message: Reason: Action: 1061 Message: Reason: Action: 1070 Message: Reason: Action: 1080 Message: Reason: Action: 1090 Message: Reason: Action: 1100 Message: Reason: Action: _______________________________________________________________________ "SHUTTER did not work properly.
- Page 38 mar345 Program Manual ______________________________________________________________________________________ Tabel continued from previous page. _______________________________________________________________________ Description _______________________________________________________________________ 1101 Message: 1102 1105 Reason: Action: 1103 Message: Reason: Action: 1110 Message: 1111 1112 1115 Reason: Action: 1215/1241 Message: 1234 1238 Reason: Action: 1239 Message: Reason: Action: _______________________________________________________________________ "No scan modes found in nb_code ..."...
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Page 39: Appendix
mar345 Program Manual ______________________________________________________________________________________ Appendix A. Configuration File Each scanner has a scanner specific configuration file. This file must reside in directory $MARTABLEDIR and is called config.XXX, where XXX is the three−digit serial number. Please refrain from changing values unless there is good reason to do so. The configuration file is a keyworded Ascii−file. -
Page 40: Calibration Files
mar345 Program Manual ______________________________________________________________________________________ B. Calibration Files Each scanner comes with 2 scanner specific calibration files. These files must reside in directory $MARTABLEDIR and are called mar2300.XXX and mar3450.XXX, where XXX is the three−digit serial number. The file contain flat field and geometrical corrections required for producing Cartesian images out of a spiral scan.
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