Compaq mar345 User's Manual
Contents
1. MARLOGDIR Location of the log output files MARHELPDIR Location of interactive help files The program relies on the correct network setup i e the mar345 scanner must be accessible by ping and telnet with IP address 192 0 2 1 For a description of the setup of the mar345 software suite see the mar345 Installation Guide 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 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 Default take N from configuration file def XXXX When starting the program go to scanmode XXXX where XXXX is 1200 1600 1800 2000 2300 2400 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 produce spiral files only transformed images more N Log output level with N20 1 2 or 3 Use more gt 0 only in case of hardware problems Default N 0 compact output noxf Spiral images will not be transformed into Cartesian images The program then requires much less memory but images cannot be displayed Default Do transform spiral images port POR2. 1 only Shortcut Ctrl i Pops up a menu with 3 choices that affect the way the image looks at zoom factors lt 1 If one pixel on the monitor corresponds to more than one pixel in the image the program will take only one image pixel to display and ignore the neighbours n th pixel or take the average of the neighbours or their maximum respectively Note that N th pixel mode is faster than the others since no calculation is involved bh Options Tear off Show resolution rings Ctrl r Hide statistics Ctri a Keep view Ctrl v Keep color scales Ctri k Reset colors Ctrict Turn On 3D plot Ctrl d Next image Ctrl n Previous image Ctri p Integrate Ctri i Zoom options mar345 Program Manual 2 7 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 Result Left Press Pops up an empty mar345 Cross section window Drag A red line is drawn from the position of the first mouse press to the position of the last mouse press Release The interpolated intensities of the pixels along the line are displayed in the mar345 Cross section window Center Press The x y coordinate intensity and resolution of the pixel is displayed in the information area in the upper left corner of the image area The right mouse button functions depend on the current zoom factor At zoom factors 1 the behaviour is a
3. cae mo 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 This window gives an overview ofthe currently programmed data sets The buttons in the lower part of the window come with different layouts Mode Left Center Right Before data Go Change Close collection really start reedit parameters Close window During data Abort NOW Stop AFTER IMAGE Close collection Aborts exposure Stops after current image Close window To start data collection you will have to press the Go button in this window During data collection the mar345 Run Parameters window monitors the progress of the data collection The window can be opened by selecting the Progress option in the Windows submenu see 3 2 1 Active data sets are highlighted Start and Image will be updated The number of oscillations is given by the multiplier in the A field If the scanner is idle this window cannot be obtained DC Set Status Images Time Distance Start 9 Ay Scanmde To go Image gc ENS BEE 3 9 Stopping Data Collection Data c
4. Action Check file sizes 73 MB and 103MB Use command catmar MARTABLEDIR mar2300 XXX to look at the calibration file header 1103 Message Scanner serial number in nb code differs from config Reason The scanner no in the file headers of files MARTABLEDIR mar2300 XXX and 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 Error writing image array 1115 Error writing image header Reason Insufficient disk space or invalid file permissions Action Clean up disk or check data directory permissions 1215 1241 Message Cannot OPEN SHUTTER at START of EXPOSURE 1234 SHUTTER was already OPEN at START of EXPOSURE 1238 Cannot CLOSE SHUTTER at END of EXPOSURE Reason X ray beam shutter damaged or dirty Otherwise the manual shutter operation switch mounted on the base may have been left in the Open state Action Check shutter and manual shutter switch on the base Open and close the shutter manually Is it very hard to operate 1239 Message STEPPER error during EXPOSURE Reason Problem with PHI axis movement Possibly software related Action Mail mar spy file Call 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 i
5. 3 Output Files The program mar345 writes all relevant messages to standard output but it also produces several types of log files depending on the configuration Since log files can be important to look at in case of software or hardware problems the program creates different versions of log files named 1 MARLOGDIR log mar log X always 2 MARLOGDIR spy mar spy X configuration file entry USE SPY 3 MARLOGDIR Ip mar ip X configuration file entry USE STATS where X is a number running from 1 to 99 All log files reside in the subdirectory assigend by the logical variable MARLOGDIR In this directory there is also a file called last log that contains only the version number of the latest i e current log file and a soft link of mar log to the latest mar log X file in subdirectory log Accordingly soft links are also set to files mar spy and mar lp if configured Up to 99 copies of the log files will be kept and then cyclically overwritten 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 MARLOGDIR up to 100 MB in total 3 mar ip Some image statistics like minimum maximum an
6. Parameters kb mar345 Change Parameters Load Copy params from Single Save Single Data Set Directory home cla data Image root xtal Scan mode 1200 1200 180 mm 0 15 Output format mar345 Collect mode TIME First image no 1 zu No ofimages 10 ee zu Exp time sec 60 Nr Oscillations Lati gt gt La a ka ka A per image Starting Q umm 4 Move Set Distance 1100 00 4 Move Set Max resolution 2 152 Ang 2 41 987 deg el 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 The amount of data sets that are offered for programming can be controlled by the configuration file entry SETS Index Crystal is a special way of collecting data with a 9 movement inbetween each image This movement is denominated increment and serves the purpose to collect a small number of images at different positions in To collect 2 images that are 90 degrees away from eachother with a oscillation of 1 0 degree for each image one will have to give an increment of 8
7. intensities average background and mean intensity over background all relative to the pixels displayed in the Image Area The background is calculated from a histogram of intensities of a box of 50x50 pixels around the center of the zoomed area Pixel values 1000 are not included in the histogram This option works for zoom factors 1 0 only 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 pp mar345 Coiors 058 siue scale Min s Max fm lax 7233 at Int 120 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 intensities are on the horizontal axis and frequency of the corresponding intensities are on the vertical 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 value given in Min left dashed bar are drawn in one color The remaining colors will be distributed in equidistant intensity ranges between Min and Max The following color schemes are used Mode lt Min gt Max All other pixel intensities Grey scales white black greys Blue scales black white blues Rainbow
8. moved using the left mouse button Right dashed red line Marks the begginning of a measured distance This line can be moved using the right mouse button Horizontal red lines Shows the length of the line in pixels mm and 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 you want to measure cell constants The program features a peak finding algorithm which tries to set the bars on top of the first and the last peak of the plot In between the peaks the program then looks for other peaks and tries to calculate the best inter peak distances by assuming a harmonic oscillation The no of peaks calculated by the program is displayed in the No of peaks text field Of course this value may be modified The derived cell constants do not take into account any particular setting or symmetry of the crystal but calculates cell constants assuming plain orthogonal axes in reciprocal space 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
9. t overlap It should be chosen such that the highest resolution of the spots is close to the edge of the scanned area i e move the detector back as far as possible This gives a better Intensity o ratio A per image The A must be chosen such that spots don t overlap If the background is large compared to the average spot intensity i e most protein crystals choose relatively small values 0 5 to 2 0 deg The smaller the better the integration works but the more exposures you need to get a complete data set Number of images 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 triclinic ones 180 deg trigonal ones 60 0 deg tetragonal ones 45 0 deg hexagonal ones about 30 0 deg and cubic ones about 25 0 deg High resolution data collections usually require a wedge of data say 20 deg at another crystal setting because of the blind region Exposure time The exposure time should be less than 30 minutes in any case because of partial decay of the F centers on the imaging plate For very weak diffractors which require longer exposure times it is better to scan one exposure after 30 min and to repeat the same exposure and add the images together later Otherwise exposure times should be chosen such that the dynamic range 0 130000 is not exceeded It is actually best to have max
10. to start data collection Distance Distance crystal to detector 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 TYPE is not used in Single Data Set mode e g images zeo 001 mar1200 1 2 30r4 in Multiple Data Set mode e g images zeo 1 001 mar1200 INDEX in Index Crystal mode e g images zeo INDEX 001 mar1200 Aor B in MAD Data mode e g images zeo A 001 mar1200 XXX is a three digit image number like 027 extension is mar1200 mar1600 mar1800 mar2000 mar2300 mar2400 mar3000 or mar345 for Output format mar345 depending on the Scan mode chosen In Index Crystal mode First image number is replaced by increment see above The starting image will always be 001 and the following images will have numbers that will be calculated from their position relative to image number 001 according to XXX i Q increment A Q 1 i 0 1 2 3 e g with increment 90 0 and A 2 0 XXX 1 46 91 136 etc mar345 Program Manual 16 In MAD Data mode No of images is replaced by No of blocks and a field for entering the number of images per 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
11. white red yellow green cyan blue purple magenta 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 lt 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 gt Max are drawn black Grey scales white Blue scales or red Rainbow Intensities which are above the saturation limit 128000 are drawn in green The dashed line in the histogram plot moves to 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 minimum The value in the Min text field is changed accordingly Right mouse button press Places the dashed red line in the histogram plot to a new position marking the maximum The value in the Max text field is changed accordingly Center mouse button drag Changes color tables Try it out to see what it really does This works for grey and blue scales only and for 8 bit color displays only Note By changing Min or Max or setting these values with the mouse button the color distribution for the whole image will be recalculated This takes some CPU time so please don t do more than one change at a time mar345 Program Manual 32 4 8 Cross Section Win
12. 345 Shutter Close in sec 80 1 min 00 00 09 mar345 Program Manual 21 3 12 Getting Help Lure EM 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 This window displays information about the current status of some pieces of the hardware in particular the current state of the erase lamps and the plate locking state It may be useful to look at this window to check wether the erase lamps are working or if the plate locks at the end of the scan 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 Unfortunately the program mar345 does not have knowledge about the generator and collimator settings so this information must be entered manually For this purpose open the mar345 X ray Setup window This window can be popped up m
13. 5 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 8 Feb 16 2000 Scanner no 049 Scanner mode 345 mm 0 15 mm Started on Wed Feb 16 15 09 08 2000 LOG file is home mar345 log log mar 1log 58 SPY file is home mar345 log spy mar spy 58 STAT file is home mar345 log lp mar 1p 58 It will also tell you if it is able to talk to the scanner If environment variables are not set you will be notified Next three windows will be created and automatically 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 not get any feed back This is because the program tries to open a network connection to the scanner and the program will sit there and wait until the scanner starts talking to it When the scanner is turned on the scanner controller will start very quickly basic network services so a ping to the address of the scanner usually 192 0 2 1 will work within 10 seconds after turning the scanner on However before starting communication with the program ma
14. 9 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 p axis moves forward and collects the same number of images in the equivalent position 180 degrees away Otherwise the items displayed in the window are as follows Item Description Title Single Data Set Multiple Data Sets or Index Crystal Directory Directory where the images will be written to Image root Name root of image files Scan mode Choice of image plate diameter to be scanned 345 300 240 or 180mm and pixelsize used 0 1mm or 0 15mm Output format Usually only 1 choice mar345 This format features a very efficient image compression that requires approx 7096 less disk space than uncompressed data Collect mode Time controlled or X ray dose controlled movement The latter one should be used on X ray sources with variable X ray flux synchrotrons 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 In DOSE mode the actual time may be different from the desired exposure time Oscillations Number of oscillations per image One oscillation is stronlgy recommended for exposure times 15 min A per image movement per image Starting position
15. SITY MIN xxx The data collection starts only if the X ray reading is above the configured value Action Check generator monochromator or 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 2100 The work in DOSE mode becomes inaccurate Action Turn down gain selector of ion chambers 1070 Message Could not recover from previous errors after X retries Reason Follow up of previous messages Action Check previous messages 1080 Message SHUTTER did not open during exposure or Shutter did not close at end of exposure Reason X ray beam shutter damaged or dirty Action Check shutter Open and close it manually Is it very hard to operate 1090 Message Scanner home position X differs from Y dy Reason Problem with radial movement of reading head Action Mail mar spy Call 1100 Message Cannot open nb code Reason File MARTABLEDIR mar2300 XXX and or MARTABLEDIR mar3450 XXX are missing or don t have read permission Action Check existence of files and permissions mar345 Program Manual 38 Tabel continued from previous page No Description 1101 Message No scan modes found in nb_code 1102 Something wrong with byteorder in nb_code 1105 No suitable scanning mode found in nb_code Reason File MARTABLEDIR mar2300 XXX and or MARTABLEDIR mar3450 XXX may be corrupted or empty
16. Single Scan 3 11 Shutter Timer 3 12 Getting Help 3 13 Hardware Status 3 14 X ray Setup 3 15 Errors and Warningsp 4 Image Display 4 1 Display Window 4 2 Menu Bar 4 3 Image Area 4 4 Workr Area 4 5 Information Areas 4 6 Window Title 4 7 Colors Window 4 8 Cross Section Window 5 Data Collection 5 1 Strategies 5 2 Checking Parameters 5 3 Warnings and Errors 5 4 End of Data Collection 6 Troubleshooting Appendix A Configuration File B Calibration Files ABER ooNOOCO A 36 39 39 40 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 Computer Requirements Motif 1 2 x shared libraries except Linux 8 16 24 32 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 variables MARTABLEDIR Location of the scanner specific calibration files mar2300 XXX and mar3450 XXX and the corresponding configuration file config XXX where XXX MAR SCANNER NO MAR SCANNER NO Three digit serial number e g 049
17. T Connect to host HOST via socket port PORT Default take PORT from configuration file usually 4441 setd The user may redefine the distance detector to crystal from within the program Default Redefining the distance is disallowed 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 This file contains essential scanner specific information For the scanner to produce valid data it is essential to have this file with all entries corresponding to valid parameters for the scanner The program mar345 will use program defaults if this file is not available c MARTABLEDIR mar2300 XXX XXX is a 3 digit serial number This file contains flat field corrections and the geometry table for transforming spiral images into Cartesian images for all scans at 0 15 mm pixelsize This file is scanner specific and required 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 103 MB See Appendix A and B for more information about input files 2
18. anually from the main window menubar or by pressing the F3 key All information given here is really not essential but it may help later on to track down problems during data processing The center of diffraction is supposed to be a physical constant for one data set and is valid for all scan modes regardless if working at 0 15 or 0 10 mm pixelsize This is why the center should not be entered in absolute pixels or millimeters referring to an origin in the lower left corner but as a deviation from the center of the image plate These values should be given in mm not in pixels and can become negative Negative x deviation means that the center of diffraction is left of the IP center A negative y deviation would be underneath the IP center p mar345 X ray Setup X ray source Rotating Anode X ray kV 50 X ray mA 100 100 FF Collimator X mm 0 3 0 3 er Collimator Y mm 03 4 Monochromator Mirrors Mirrors Beam polarization 0 000 Deviation of beam center from IP center IP center x 0 y 0 Deviation X Y mm 0 000 0 000 Remarks NENNEN 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 Some
19. ase 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 2 Zoom Buttons UE By pressing the full image button the image will be displayed such that it fits ot entirely into the window The other buttons will zoom in or zoom out 4 4 3 Colors Q The upper text field has the same function as the Max field in the mar345 Colors window and the lower text field corresponds to the Min field see chapter 4 9 Dragging the center mouse button in the color area the color distribution changes Try it out to see what happens This 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 image area the x y coordinate intensity and resolution of the pixel under the pointer is displayed Lower left corner Once an image has been loaded successfully some information wavelength distance maximum intensity and average intensity is displayed unless Hide statistics was pressed see 4 2 2 Upper right corner When pressing the Integrate button in the Options submenu see 4 2 2 the following information is displayed number of pixels in x and y maximum minimum and average intensity sum of pixel intensities standard deviation of
20. d average intensity Normally these values are not of much interest so USE STATS should rather be the exception 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 Send commands to the scanner Receive information from the scanner 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 Ethernet interface Usually the host computer features a dedicated Ethernet card for communicating with the scanner Host computer and scanner are linked via a so called cross over cable i e a special RJ 45 type cable that allows for directly connecting 2 computers without the need of a hub Transformation and data display requires some memory as well as CPU time Typically mar345 keeps the equivalent of 2 5 images in memory When using 3450x3450 pixel images this corresponds to 75 MB Data collection should always have highest priority However there is no real protection against abuse of the computer by other processes In particular memory consuming data processing jobs can cause drops in performance of the workstation to such a degree that nothing else will work Also network I O can severly degrade the host computer performance e g when processing data across NFS mounted disks mar34
21. dow kb mar345 Cross Section Close Mo ofpeaks a AMT xY 303 499 gt 270 604 Angle 342 55 Maxl 4853 Minl 354 Avgl 809 Sigl 927 0 1 3 27 4 53 67 80 3 10 83 12 4 X EE 0 0 2 0 40 60 80 10 0 12 0 14 0 16 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 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 constant is calculated from the distance between the two dashed lines and the number of peaks The result is displayed in the message area Message area Shows the coordinates of the start and end of the line the angle with the base line maximum minimum average and standard deviation of the intensities along the drawn line When changing the no of peaks manually the second line displays the derived cell constant 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
22. e Error sending command to mar controller Reason Network connection to scanner interrupted Action Reboot scanner Check cables Try ping mar345 1001 Message SERVO system cannot be INITIALIZED Reason Severe hardware problem Action Call 1010 Message Waiting for X rays Reason The X ray intensity as read from the ion chamber has dropped below the critical level see configuration file INTENSITY MIN xxx The next exposure starts only after the X rays are back Action Check generator monochromator or collimator 1020 Message Not enough disk space left on device Aborting data collection Reason Disk full Action Clean up disk 1030 Message The Image Plate has been exposed to X rays Reason A running exposure has been aborted Action Erase plate and continue 1040 Message Ximages have been successfully retaken Reason Some images had to be retaken due to hardware problems possibly shutter Action Carefully check log file for learning more about the reasons mar345 Program Manual 37 Tabel continued from previous page No Description 1050 Message SHUTTER did not work properly Abandoning data collection Reason X ray beam shutter damaged or dirty Action Check shutter Open and close it manually Is it very hard to operate 1060 Message X ray reading too low Reason The X ray intensity as read from the ion chamber is below the critical level see configuration file INTEN
23. e clafog sets x2 set mar345 Change Parameters window Select a file by double clicking or by pressing the Load button Selected File homelclallog sets Load Filter Cancel mar345 Program Manual 18 3 7 Moving Distance and Phi The detector position and the axis can be moved by pressing buttons in 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 Starting and Distance 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 dangerous in case of the detector movement so for the distance this button works only if the program has been started with the command line argument setd In any case confirmation of the desired action is required If you really want to move Distance or the mar345 Stop window pops up and stays on the screen until the action has finished During this time you are not allowed to make any further input to the program The only possible action is pressing the Stop button in the mar345 Stop window p mar345 Stop To interrupt press STOP 1 2 kb mar345 Distance Phi a 90 Move a0
24. ened if there is enough disk space etc 5 3 Errors and Warnings In case of computer or scanner problems warning messages will be printed on standard output and in the log file Very important messages will also be displayed in a special window Problems fall into 3 categories fatal errors warnings and notifications See chapter Troubleshooting for more details 5 4 End of Data Collection After having finished a data set mar345 writes a summary into the corresponding data directory The summary files come in 2 formats image root SUMMARY plain Ascii text file image root html Ascii file with HTML formatting instructions These files should be printed and archived 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 gt 1000 are generated by program mar345 and may be a consequence of a controller error or some other kind of malfunctioning or warning If you don t know how to fix a scanner problem contact marresearch We will usually ask you right away to send us the mar spy file and the mar log file where the error occured see chapter 2 3 since they contain almost all information we need The following error messages 1000 are produced by program mar345 No Description 1000 Messag
25. idea to collect only single images at one position since the detector will have to move very often and that takes time Finally one ends up with 2 contiguous data sets A and B both covering the same range but differing by 180 degrees For your convenience all text fields are followed by a menu with preset values The menus can be activated by using the left mouse button Most of the option menus are followed by up and down arrows that will increment or decrement the currently displayed values by one unit In Multiple Data Set mode the following buttons are added underneath the Distance field Selected set 1 2 2 EM gt gt Pase m ar T EN Sot Erase frst _Sance 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 at the top of the window will also tell you which of the sets you are programming Even if you have edited one of the data sets you don t actually have to use it The Status of a programmed data set can be set to Use green or Skip red Default is Skip When more than 4 programmable data sets are configured entry SETS in the configuration file one may move forwards and backwards to the next or previous 4 sets using the gt gt and lt lt buttons respectively Note 1 All changes are saved automatically to file mar345 dat in directory MARLOGDIR and are available
26. imum intensities considerably less e g 60000 Number of oscillations Best to leave at 1 except when using exposure times larger than 15 minutes Scan mode Why scan the 345 mm plate if there is not enough diffraction A 180 mm scan takes half the time to scan needs 80 less disk space and 80 less processing time 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 1096 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 Output format Use of mar345 format is strongly suggested A mar345 file typically requires 70 less disk space than a standard uncompressed image file All major protein data processing packages support this format Collect mode Use TIME mode unless on synchrotrons For indexing crystals usually 2 images that differ from each other by a movement in of 90 degrees gives 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 a consistency check of the input parameters In most cases the program will tell you if the input parameters really do not make sense It checks wether files can be op
27. mar research mars 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 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 prior written consent of X ray Research G m b H Possession use or copying of the software described in this publication is authorized only pursuant to a valid written license from X ray Research G m b H marresearch and the marresearch logo are registered trademarks of X ray Research G m b H mar345 Program Manual Contents 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 8 Starting Data Collection 3 9 Stopping Data Collection 3 10
28. ollection can be stopped by pressing the Stop button in the main window or by pressing the Stop or Abort button in the mar345 Run Parameters window If the scanner is scanning or erasing the imaging plate this cycle will always be finished Pressing Abort in this moment will be the same as pressing Stop Otherwise Abort closes the X ray beam shutter immediately and stops or distance movement mar345 Program Manual 20 3 10 Single Scan LUE ae Se Directory Jnomeiclaidata Image root Scan mode 2300 2300 345 mm 0 15 Image number fa AY 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 drives the scanning head to the desired position 3 11 Shutter Timer The X ray beam shutter can be operated manually although normally there should not be any requirement to do this When operating the shutter manually it can be useful to know how long time the shutter is open When opening the mar345 Shutter Timer window shortcut F4 the program starts counting how long time the shutter is open One may enter a closing time in seconds When this time period has elapsed the shutter closes automatically kb mar
29. pointer was in the main window The Options menu features the following buttons Show Hide resolution rings Toggles display of resolution rings Shortcut Ctrl r Show Hide statistics Toggles display of image statistics The statistics about maximum intensity and average intensity in the image as well as the wavelength and distance are normally displayed in the lower left corner of the image area Shortcut Ctrl a Do not Keep view Normally if a new image is loaded the program displays the entire image and also calculates the best color scheme If you want to look at all images in the very same way select Keep view Shortcut Ctrl v mar345 Program Manual Do not Keep color scales Reset colors Turn On Off 3D plot Next image Previous image Integrate Zoom options 26 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 Recalculates colors and redisplays the image Shortcut Ctrl t Toggles 3 D representation of magnified areas of the image Available only at zoom factors gt 4 Shortcut Ctrl d Load the next image i e increment image number by 1 Shortcut Ctrl n Load the previous image i e decrement image number by 1 Shortcut Ctrl p Pixels in the image area are integrated and the results are displayed in the upper right corner of the image area Works for zoom factors gt
30. r345 the scanner must do first some initialization i e drive the scanning head to its default position scan mode 2300 and lock the plate Only when the plate is successfully locked cling program mar345 can start talking to the scanner You may however start the program first and then turn on the scanner The program really waits until a connection can be established mar345 Program Manual 9 DEZE gr Windows Help 3 User Interface Menu Wr marresearch 3 1 Main Window Thu 15 21 Time until End of Data Set 01 46 26 to go D Current Time Scannin Shutter is CLOSED a Current Image xtal_001 Current Mode Progress Bar 345 mm 0 15 u ENS D Current Distance Shutter is OPEN f 100 00 Current Phi Shutter Status Scanner Status Area Intensity 15 00 Collect Menu Free Disk Space 2116 MB P di Scan Erase CANCEL eS Ecd Br IX NL initialize Scanner Command Area Open Shutter Quit Hi 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 1 Windows Submenu The Windows submenu pops up if the Windows button in the menu bar was pressed or if Alt
31. rent Mode Current Distance Current Phi Intensity Free disk space During data collection this field shows the time it takes to finish all active or queued data sets Displays local computer time If the scanner is performing an operation the progress of this operation will be displayed with a colored progress bar and an appropriate text string Shows the state of the local X ray beam shutter open or closed Shows the name of the current image leaving out the directory and file name extension Shows the current scanmode of the scanner Shows the current distance of detector to crystal Shows the current position of the PHI axis Displays the current intensity reading of the selected ionization chamber Shows how many MB of disk space are available on the disk where the current image will be written to Under normal conditions the program retrieves status information from the scanner once a second The time and the free disk space will be updated less frequently 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 areasonable speed 3 4 Scanner Command Area The buttons in the command area can be used to send commands directly to the scanner or to pop
32. s follows Button Action Result Right Press Marks one corner of a zoom area Drag A red box is drawn from the position of the first mouse press to the position of the last mouse press Release The pixels contained in the red box are displayed in the Image Area The magnification factor depends on the size of the box and the size of the window At zoom factors gt 1 the currently displayed magnified part of the image will be recentered at the position where the right mouse button has been pressed By this method one can move around in the image by always recentering at new positions mar345 Program Manual 28 At zoom factors gt 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 In the 3D plot one may rescale the peaks using the minimum and maximum intensity field on the y axis of the plot fhome clafacasdatailysoimgAyso_2 001 marl200 1200 pixels pixels 71x63 x 402 gt 464 y 810 gt 880 Minl 298 821 832 843 854 865 876 mar345 Program Manual 29 4 4 Work Area ELI 4 4 1 Load Buttons In By pressing the single left or right arrow one can decrease or incre
33. s 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 Please refer to the man page mar345_config_file for a full description of keywords A typical configuration file looks like this Configuration file for scanner no 120 1 1 1 Only modify the following keywords if desired DIST MIN 75 30 MAX 426 30 INTENSITY MIN 2 0 WARN 20 0 USE SPY USE STATS USE INCR USE RUN USE HTML USE SUMMARY COLORS 64 SETS 4 WAVE 1 541789 ONOCHROMATOR Mirrors GENERATOR Rotating anode NETWORK PORT 4441 HOST 192 0 2 1 ODE 2300 ROFF 180 ADC 50 AADD 42 BADD 45 ODE 2000 ROFF 180 ADC 50 AADD 42 BADD 45 ODE 1600 ROFF 180 ADC 50 AADD 42 BADD 45 ODE 1200 ROFF 180 ADC 50 AADD 42 BADD 45 ODE 3450 ROFF 180 ADC 50 AADD 42 BADD 45 ODE 3000 ROFF 180 ADC 50 AADD 42 BADD 45 ODE 2400 ROFF 180 ADC 50 AADD 42 BADD 45 ODE 1800 ROFF 180 ADC 50 AADD 42 BADD 45 IP Diameter 345mm 300mm 240mm 180mm GAPS 89615 78601 63852 49103 02 2 2000 GAPS valid for S N 120 mar345 Program Manual B Calibration Files 40 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 fla
34. t 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 15mm modes 2300 2000 1600 and 1200 and has a typical size of 73 MB File mar3450 XXX is used for scans at pixelsizes of 0 10mm modes 3450 3000 2400 and 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 this Format type mar 345 Line At byte Contents improve Version 2 8 4 192 PROGRAM 5 256 DATE Wed 6 320 SCANNER 120 7 384 PIXEL LEN 8 448 PHIOFF 269 9 512 CUTOFF 0 0 10 576 SCALE 327 11 640 GAT 1 0 T2 704 UMBER PIX 13 768 ODE 230 14 832 ODE 200 15 896 ODE 160 16 960 ODE 120 17 1024 ODE 230 18 1088 ODE 200 19 1152 ODE 160 20 1216 ODE 120 Feb 2 12 00 40 2000 GTH 75 HEIGHT 150 970 00 67 000 00 0X 0 Y 1149 0x 0 Y 999 0X 0 Y 800 0X 0 Y 600 0 PIX 7766361 0 PIX 5956761 0 PIX 3845618 0 PIX 2190418 ROFF ROFF ROFF ROFF POS POS POS POS SUBPIXELS 25 0 0 0 0 4096 ELS 7766361 NEIGHBOURS 25199739 SKIP 144 SKIP 144 SKIP 809 SKIP 809 17151502 37076767 52798207
35. the next time mar345 is used Note 2 synchrotons only Since wavelength varies on synchrotron sources the configuration file should contain the keyword wavelength variable In this case there is an additional input field for the used wavelength underneath the Distance field Make sure that the correct wavelength is entered since this information is written into image headers and programs like marView rely on it 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 To save parameters press the Save button in the mar345 Change Parameters window kb mar345 Save Set Directory fhome claflog sets File root xtal Data set Single Set d Multiple Data Sets _ Index Crystal J MAD Data Set bh f mar345 Load Set One now has the choice of saving only some sets of programmed Search Pattern parameters or all of them By default the files to be saved will Ihomeiclallogisets se be written into directory MARLOGDIR sets The filename will always be File root set Parameter Files fhome clafog sets x1 set fhome clafog sets x11 set To retrieve parameters press the Load button in the fhom
36. up further windows i e the mar345 Scan and mar345 Change Parameters windows The functions of the individual buttons are Button Description Collect Changes layout of the button choices i e the Collect Menu buttons are displayed Scan Pops up the mar345 Scan window Erase Immediately starts to erase the imaging plate Erasing is identical to doing a scan 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 scanner looses the information about the distance for some reasons The re ference positions are taken from the configuration file The detector move ment has to be confirmed The configuration file will be reread when pressing this button Open Shutter Opens or closes the local X ray beam shutter And in the Collect Menu there are Single Set Pops up the mar345 Change Parameters window for programming a single data set Multiple Sets Pops up the mar345 Change Parameters window for programming up to 64 data sets Index Crystal Pops up the mar345 Change Parameters window for programming a small number of images to be used for indexing a crystal MAD Data Pops up the mar345 Change Parameters window for programming a data collection typical for anomalous and or MAD data Cancel Returns to the original layout mar345 Program Manual 3 5 Editing Data Collection
37. w was pressed while the pointer was in the main window The Windows submenu features the following buttons b Windows Tear off Display Pops up the mar 345 Display window Display F1 Shortcut F1 Progress F2 Progress Pops up the mar345 Progress window X ray Setup F3 h F2 un Shutter Timer F4 X ray Setup Pops up the mar345 Setup window E Shortcut F3 Log file F5 Hardware Status F6 Shutter Timer Pops up the mar345 Shutter Timer window Shortcut F4 Error Window F7 Log file Pops up the mar345 Help window and Move Distance F8 displays the current log file Shortcut F5 Move PHI F9 Hardware Pops up the mar345 Hardware Status Status window Shortcut F6 Reset Scanner Ctrler Error Window Pops up the mar345 Error window and Quit Ctrl q displays the current errors Shortcut F7 mar345 Program Manual Move Distance Move Phi Reset Scanner Quit 11 Pops up the mar345 Distance window Shortcut F8 Pops up the mar345 Phi window Shortcut F9 Reboots the scanner reboot Shortcut Ctrl r 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 interface changes dynamically according to the current scanner operation It features the following items Item Description marresearch Time until End Current Time Progress Bar Shutter Status Current Image Cur
38. warnings and errors may have an obvious solution if they are not related to the scanner hardware For latter ones please refer to section Troubleshooting HEZE Thu Feb 24 15 30 05 Ihome cla data xtal 002 mar1200 mar345 Program Manual 24 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 d home cla aca data ysoAmg lyso 2 001 mar1200 1200 pixels Windows Options Help F X 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 1 Windows Submenu The Windows submenu pops up when the Windows button in the menu bar was pressed or if Alt w was pressed while the pointer was in the main window The submenu is a so called tear off menu The Windows menu features the following buttons Files Pops up the mar345 Files window b Windows Te Shortcut Ctrl f Files Ctri f Colors Pops up the mar345 Colors window Shortcut Ctrl c Colors Ctrl e Close Closes the display window Close F1 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 0 was pressed while the
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