mar research The Program Manual By Dr. Claudio Klein X−ray Research G.m.b.H. Tel.: (+49) (40) 529−884−0 Segeberger Chaussee 34 Fax: (+49) (40) 529−884−20 D−22850 Norderstedt Mail: info@marresearch.com Germany Web: www.marresearch.
mar345 Program Manual 2 ______________________________________________________________________________________ The mar345 Program Manual Version 2.0 February 24, 2000 Written by Dr. Claudio Klein Copyright 2000 X−Ray Research G.m.b.H. All Rights Reserved. This document contains proprietary and confidential information of X−ray Research G.m.b.H..
mar345 Program Manual 3 ______________________________________________________________________________________ Contents 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 3.6 Loading and Saving Data Collection Parameters 3.7 Moving Distance and Phi 3.
mar345 Program Manual 4 ______________________________________________________________________________________ 1. Introduction The program mar345 is a fully menu driven graphical user interface (GUI) for collecting and displaying images on a mar345 imaging plate system. The program is provided as binary executable for several computer platforms and operating systems: − Silicon Graphics: − Digital: − Linux: IRIX 5.x, 6.x Compaq Tru Unix 4.x, 5.x RedHat 5.x, 6.x, SuSE 6.x 1.
mar345 Program Manual 5 ______________________________________________________________________________________ 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 [−h] [−colors N] [−def XXXX] [−host HOST] [−keep] [−more N] [−noxf] [−port PORT] [−setd] The command line options are: −h Print a usage summary −colors N Use N colors for drawing images.
mar345 Program Manual 6 ______________________________________________________________________________________ 2.2 Input Files The program mar345 requires the following input files to work properly: a) $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. b) $MARTABLEDIR/config.XXX XXX is a 3−digit serial number.
mar345 Program Manual 7 ______________________________________________________________________________________ The contents of the different types of log files are as follows: 1.) mar.log: All messages on the terminal output. 2.) mar.spy: Native mar345 controller messages. These messages become very important in case of hardware problems. Therefore, USE SPY should always be set.
mar345 Program Manual 8 ______________________________________________________________________________________ 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 : mar345 Version : 2.0.
mar345 Program Manual 9 ______________________________________________________________________________________ 3. User Interface Menu Bar 3.
mar345 Program Manual 10 ______________________________________________________________________________________ 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). Shortcut: Alt+w. Help Pops up the mar345−Help window. Shortcut: F5. 3.2.
mar345 Program Manual 11 ______________________________________________________________________________________ Move Distance Pops up the mar345−Distance window. Shortcut: F8. Move Phi Pops up the mar345−Phi window. Shortcut: F9. Reset Scanner Reboots the scanner reboot. Shortcut: Ctrl+r. Quit Quits program. Shortcut: Ctrl+q. 3.3 Scanner Status Area The status area provides at all times all necessary information about the current status of the scanner.
mar345 Program Manual 12 ______________________________________________________________________________________ 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. 3.
mar345 Program Manual 13 ______________________________________________________________________________________ 3.
mar345 Program Manual 14 ______________________________________________________________________________________ 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 − Index Crystal − MAD Data The difference is, that in Multiple Data Sets one can program up to 64 data sets with the full range of parameters.
mar345 Program Manual 15 ______________________________________________________________________________________ Table continued from previous page. _______________________________________________________________________ Item Description ________________________________________________________________________ First image no. Image number of first image. Range is 1 through 999. No. of images Number of images to be collected. Range is 1 through 999. Exp. time Exposure time in seconds.
mar345 Program Manual 16 ______________________________________________________________________________________ In MAD Data mode "No. of images" is replaced by "No. of ϕ blocks" and a field for entering the number of images per ϕ block. It is supposed that one wants to collect a number of contiguous images at a certain position and then the same wedge of data 180 degrees away.
mar345 Program Manual 17 ______________________________________________________________________________________ 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.
mar345 Program Manual 18 ______________________________________________________________________________________ 3.7 Moving Distance and Phi The detector position and the ϕ axis can be moved by pressing buttons in the mar345−Change Parameters window. One can also get separate windows for moving "ϕ" 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.
mar345 Program Manual 19 ______________________________________________________________________________________ 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.
mar345 Program Manual 20 ______________________________________________________________________________________ 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. Instead of a scan one can do an erase cycle.
mar345 Program Manual 21 ______________________________________________________________________________________ 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" submenu (shortcut is: Alt+t). 3.13 Hardware Status The mar345−Hardware Status window can be popped up from the main window menubar or by pressing the F6 key.
mar345 Program Manual 22 ______________________________________________________________________________________ 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. It might, however, be useful to add also some information about the state of the X−ray source.
mar345 Program Manual 23 ______________________________________________________________________________________ 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.
mar345 Program Manual 24 ______________________________________________________________________________________ 4. Image Display 4.1 Display Window The image display window controls the most important display functions.
mar345 Program Manual 25 ______________________________________________________________________________________ 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.
mar345 Program Manual 26 ______________________________________________________________________________________ Do not/Keep color scales 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" Shortcut: Ctrl+k Reset colors Recalculates colors and redisplays the image. Shortcut: Ctrl+t Turn On/Off 3D−plot Toggles 3−D representation of magnified areas of the image.
mar345 Program Manual 27 ______________________________________________________________________________________ 4.3 Image Area In this area, the image is displayed. With the pointer (3−way mouse button) several additional functions can be accessed.
mar345 Program Manual 28 ______________________________________________________________________________________ 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.
mar345 Program Manual 29 ______________________________________________________________________________________ 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. 4.4.
mar345 Program Manual 30 ______________________________________________________________________________________ 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. The window provides a drawing area showing a histogram of intensity values found in the image, i.e.
mar345 Program Manual 31 ______________________________________________________________________________________ The functions of the mar345−Colors window widgets are: Grey scales Selection of coloring mode. Alternatives: Blue scales, Rainbow. Min All pixels with intensities <= Min are drawn white (black in Blue scales). The dashed line in the histogram plot moves to the specified value. Max All pixels with intensities >= Max are drawn black (Grey scales), white (Blue scales) or red (Rainbow).
mar345 Program Manual 32 ______________________________________________________________________________________ 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. of peaks Specifies the number of peaks between the two dashed lines in the plot area of the mar345−Cross section window.
mar345 Program Manual 33 ______________________________________________________________________________________ The plot area of the window shows the following features: Vertical axis Interpolated intensities Upper horizontal axis Length of line in pixel units. Lower horizontal axis Length of line in mm units. Left dashed red line Marks the begginning of a measured distance. This line can be moved using the left mouse button. Right dashed red line Marks the begginning of a measured distance.
mar345 Program Manual 34 ______________________________________________________________________________________ 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.
mar345 Program Manual 35 ______________________________________________________________________________________ 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. So the decision is some kind of compromise.
mar345 Program Manual 36 ______________________________________________________________________________________ 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.
mar345 Program Manual 37 ______________________________________________________________________________________ Tabel continued from previous page. _______________________________________________________________________ No. Description _______________________________________________________________________ 1050 Message: Reason: Action: "SHUTTER did not work properly. Abandoning data collection" X−ray beam shutter damaged or dirty. Check shutter. Open and close it manually.
mar345 Program Manual 38 ______________________________________________________________________________________ Tabel continued from previous page. _______________________________________________________________________ No.
mar345 Program Manual 39 ______________________________________________________________________________________ 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.
mar345 Program Manual 40 ______________________________________________________________________________________ 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. − File mar2300.XXX is used for scans at pixelsizes of 0.