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mar345 Program Manual

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3.5 Editing Data Collection Parameters

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Summary of Contents for Graphical User Interface mar345

Page 1: ...search 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 The Program Manual By Dr Claudio Klein mar...

Page 2: ...ary 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 wr...

Page 3: ...ng and Saving Data Collection Parameters 17 3 7 Moving Distance and Phi 18 3 8 Starting Data Collection 19 3 9 Stopping Data Collection 19 3 10 Single Scan 20 3 11 Shutter Timer 20 3 12 Getting Help 2...

Page 4: ...bit colors X windows terminal with 1280x1024 pixels Standard Helvetica and Symbol fonts 96 MB RAM memory or more 1 2 Environment The program relies on definitions of the following environment variable...

Page 5: ...400 3000 or 3450 Default stay in current scan mode host HOST Connect to host HOST Default take HOST from configuration file usually 192 0 2 1 keep Spiral images will be saved on disk Default do not pr...

Page 6: ...ed to do scans in 0 15 mm pixel modes The typical size of this file is 73 MB d MARTABLEDIR ma3450 XXX Same as mar23000 XXX but used for all scans at 0 10 mm pixelsize The typical size of this file is...

Page 7: ...Transform spiral images into Cartesian images Display transformed images User input is done via the graphical user interface see chapter 3 Communication with the scanner is realized through an Etherne...

Page 8: ...omatically placed on the screen a startup window the mar345 main window and an empty image display window If the scanner is not turned on at all by invoking program mar345 on the command line you will...

Page 9: ..._________________________________________________________________________ 3 User Interface 3 1 Main Window Menu Bar Scanner Status Area Scanner Command Area Collect Menu Progress Bar Shutter Status Ti...

Page 10: ...enu pops up if the Windows button in the menu bar was pressed or if Alt w was pressed while the pointer was in the main window The Windows submenu features the following buttons Display Pops up the ma...

Page 11: ...h all active or queued data sets Current Time Displays local computer time Progress Bar If the scanner is performing an operation the progress of this operation will be displayed with a colored progre...

Page 12: ...can but no data are taken Initialize The scanner will move to its distance reference position usually at the far end of the translation stage This distance initialization may have to be done if the sc...

Page 13: ...mar345 Program Manual 1 3 ______________________________________________________________________________________ 3 5 Editing Data Collection Parameters...

Page 14: ...increment of 89 0 degrees MAD Data is a special way of collecting data with anomalous signals In this mode a number of images is collected then the axis moves forward and collects the same number of...

Page 15: ...____________________________ 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 a...

Page 16: ...nderneath the Distance field You may toggle between different data set parameters by pressing the corresponding Selected Set button The currently selected set will be highlighted and the title string...

Page 17: ...tore a typical set of data collection parameters to a file and retrieve the parameters when desired To save parameters press the Save button in the mar345 Change Parameters window One now has the choi...

Page 18: ...tance are both followed by two additional buttons Pressing Move will tell the scanner to move the detector or the motor to the desired position Set will redefine the currently known value This can be...

Page 19: ...During data Abort NOW Stop AFTER IMAGE Close collection Aborts exposure Stops after current image Close window ________________________________________________________________________ To start data c...

Page 20: ...followed by an erase Instead of a scan one can do an erase cycle Change Mode only drives the scanning head to the desired position 3 11 Shutter Timer The X ray beam shutter can be operated manually al...

Page 21: ...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 This w...

Page 22: ...ed manually For this purpose open the mar345 X ray Setup window This window can be popped up manually from the main window menubar or by pressing the F3 key All information given here is really not es...

Page 23: ...r 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...

Page 24: ..._________________________________________________________ 4 Image Display 4 1 Display Window The image display window controls the most important display functions It consists of different areas Work...

Page 25: ...p the mar345 Colors window Shortcut Ctrl c Close Closes the display window Shortcut F1 4 2 2 Options Submenu The Options submenu pops up when the Options button in the menu bar was pressed or if Alt o...

Page 26: ...next image i e increment image number by 1 Shortcut Ctrl n Previous image Load the previous image i e decrement image number by 1 Shortcut Ctrl p Integrate Pixels in the image area are integrated and...

Page 27: ...ed in the information area in the upper left corner of the image area ________________________________________________________________________ The right mouse button functions depend on the current zo...

Page 28: ...r 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 bu...

Page 29: ...s doesn t work for Rainbow mode see below and it doesn t work on 16 24 32 bit color screens only with 8 bit colors 4 5 Information Areas Upper left corner When pressing the center mouse button in the...

Page 30: ...axis The histogram is used to distribute colors or greyscales The program tries to use 64 colors All pixels with intensities larger than the value given in Max right dashed bar or smaller than the va...

Page 31: ...o the specified value In the histogram plot the mouse buttons have the following functions Left mouse button press Places the dashed red line in the histogram plot to a new position marking the minimu...

Page 32: ...two dashed lines in the plot area of the mar345 Cross section window Use the arrows on the right hand side of the text field to increment or decrement the value by 1 When pressed the real space cell...

Page 33: ...the distance between the dashed vertical lines The pointer can be used to measure distances by setting the red dashed lines to the desired position along the drawn line This is particularly useful if...

Page 34: ...ges How many images you need depends on the symmetry of the space group and on the setting of the crystal As a rule of thumb orthorhombic crystals require 90 0 deg of data monoclinic ones 120 deg tric...

Page 35: ...es good results In the case of very small molecules i e cell axes of about 10 deg you may not get enough spots from 2 images only 5 2 Checking Parameters Before starting a data collection mar345 makes...

Page 36: ...________________________________________________________ 1000 Message Error sending command to mar controller Reason Network connection to scanner interrupted Action Reboot scanner Check cables Try pi...

Page 37: ...collimator 1061 Message X rays reading too high for DOSE mode Reason The X ray intensity as read from the ion chamber shows very large numbers 100 The work in DOSE mode becomes inaccurate Action Turn...

Page 38: ...or MARTABLEDIR mar3450 XXX are not identical to MAR_SCANNER_NO The calibration files may not belong to the scanner Action Call 1110 Message Cannot create image file 1111 Cannot open image file 1112 E...

Page 39: ...___________ Configuration file for scanner no 120 ______________________________________ Only modify the following keywords if desired DIST MIN 75 30 MAX 426 30 INTENSITY MIN 2 0 WARN 20 0 USE SPY USE...

Page 40: ...1800 and has a typical size of 103 MB Both files are binary files They feature an Ascii file header that can be looked up using program catmar A typical output of command catmar mar2300 120 looks like...

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