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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.com
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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.. 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
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mar345 Program Manual 3 ______________________________________________________________________________________ Contents 1 Introduction 4 1.1 Computer Requirements 4 1.2 Environment 4 2 Running mar345 5 2.1 Command Line 5 2.2 Input Files 6 2.3 Output Files 6 2.4 Basic Concept and Rules 7 2.5 Starting Up 8 3 User Interface 9 3.1 Main Window 9 3.2 Menu Bar 10 3.3 Scanner Status Area 11 3.4 Scanner Command Area 12 3.5 Editing Data Collection Parameters 13 3.6 Loading and Saving Data
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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: IRIX 5.x, 6.x − Digital: Compaq Tru Unix 4.x, 5.x − Linux: RedHat 5.x, 6.x, SuSE 6.x 1.1 Compu
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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
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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−digi
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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. Note, that these files can become very large in size, so sufficient disk space should be available in
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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: ============================================================= Prog
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mar345 Program Manual 9 ______________________________________________________________________________________ 3. User Interface Menu Bar 3.1 Main Window Time until End of Data Set Current Time Progress Bar Shutter Status Scanner Status Area Collect Menu Scanner Command Area
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mar345 Program Manual 1 0 ______________________________________________________________________________________ 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. 3.2.1 Windows Submenu The Windows submenu pops
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mar345 Program Manual 1 1 ______________________________________________________________________________________ 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.This part of the user int
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mar345 Program Manual 1 2 ______________________________________________________________________________________ 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. 3.4 Scanner Command Area The buttons in the command area can be used
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mar345 Program Manual 1 3 ______________________________________________________________________________________ 3.5 Editing Data Collection Parameters
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mar345 Program Manual 1 4 ______________________________________________________________________________________ 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. The amount
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mar345 Program Manual 1 5 ______________________________________________________________________________________ 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 secon
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mar345 Program Manual 1 6 ______________________________________________________________________________________ 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. It is not such a good idea to collect only single images at one ϕ position since the detector will have
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mar345 Program Manual 1 7 ______________________________________________________________________________________ 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. To save parameters, press the "Save" butto
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mar345 Program Manual 1 8 ______________________________________________________________________________________ 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 windo
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mar345 Program Manual 1 9 ______________________________________________________________________________________ 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.
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mar345 Program Manual 2 0 ______________________________________________________________________________________ 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. "Change Mode" only dri
