mar research
The
Program Manual
By Dr. Claudio Klein
X−ray Research G.m.b.H.
Tel.: (+49) (40) 529−884−0
Fax: (+49) (40) 529−884−20
Mail: [email protected]
Segeberger Chaussee 34
D−22850 Norderstedt
Germany
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Contents
1 Introduction
1.1 Computer Requirements
1.2 Environment
4
4
4
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
5
5
6
6
7
8
3 User Interface
3.1 Main Window
9
9
3.2 Menu Bar
10
11
12
13
17
18
19
19
20
20
21
21
22
23
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 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
24
24
25
27
29
29
30
30
32
5 Data Collection
5.1 Strategies
5.2 Checking Parameters
5.3 Warnings and Errors
5.4 End of Data Collection
34
34
35
35
35
6 Troubleshooting
36
Appendix
A Configuration File
B Calibration Files
39
39
40
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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
1.1 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 ).
Three digit serial number, e.g. 049.
− MAR_SCANNER_NO
− 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".
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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
−keep
Connect to host HOST.
Default: take HOST from configuration file (usually 192.0.2.1)
Spiral images will be saved on disk.
Default: do not produce spiral files, only transformed images.
−more N
Log output level with N=0, 1, 2 or 3.
Use more > 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 PORT
−setd
Connect to host HOST via socket port PORT.
Default: take PORT from configuration file (usually 4441)
The user may redefine the distance detector to crystal from
within the program.
Default: Redefining the distance is disallowed..
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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.
2.3 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
2.) $MARLOGDIR/spy/mar.spy.X
3.) $MARLOGDIR/lp/mar.lp.X
(always)
(configuration file entry: USE SPY)
(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.
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The contents of the different types of log files are as follows:
1.) mar.log:
2.) mar.spy:
All messages on the terminal output.
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.lp:
Some image statistics like minimum, maximum and 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!
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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
Version
:
:
mar345
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.log.58
SPY file is: /home/mar345/log/spy/mar.spy.58
STAT file is: /home/mar345/log/lp/mar.lp.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 mar345, 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.
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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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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
Help
Pops up the Windows submenu (3.2.1).
Shortcut: Alt+w.
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+w" was pressed
while the pointer was in the main window.
The Windows submenu features the following buttons:
Display
Pops up the mar 345−Display window.
Shortcut: F1.
Progress
Pops up the mar345−Progress window.
Shortcut: F2.
X−ray Setup Pops up the mar345−Setup window.
Shortcut: F3.
Shutter Timer Pops up the mar345−Shutter Timer
window. Shortcut: F4.
Log−file
Pops up the mar345−Help window and
displays the current log file. Shortcut: F5.
Hardware
Status
Pops up the mar345−Hardware Status
window. Shortcut: F6.
Error Window Pops up the mar345−Error window and
displays the current errors. Shortcut: F7.
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Move Distance
Move Phi
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.
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. It features the following items:
_______________________________________________________________________
Item
Description
________________________________________________________________________
marresearch /
Time until End
During data collection, this field shows the time it takes
to finish all active or queued data sets.
Current Time
Progress Bar
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.
Shutter Status
Current Image
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.
Current Mode
Current Distance
Current Phi
Shows the current scanmode of the scanner.
Shows the current distance of detector to crystal.
Shows the current position of the PHI axis.
Intensity
Displays the current intensity reading of the selected
ionization chamber.
Free disk space
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.
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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 to send commands directly to the scanner or
to pop 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
Cancel
Pops up the mar345−Change Parameters window for programming
a data collection typical for anomalous and/or MAD data.
Returns to the original layout.
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3.5 Editing Data Collection Parameters
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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 ϕ movement inbetween each image.
This ϕ movement is denominated "ϕ increment" and serves the purpose to collect a small
number of images at different positions in ϕ.To collect 2 images that are 90 degrees away
from eachother with a ϕ oscillation of 1.0 degree for each image one will have to give an
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 ϕ 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:
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Item
Description
________________________________________________________________________
Title
Single Data Set, Multiple Data Sets or Index Crystal.
Directory where the images will be written to.
Name root of image files.
Directory
Image root
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
Collect mode
Usually only 1 choice: mar345. This format features a very
efficient image compression that requires approx. 70% less
disk space than uncompressed data.
Time controlled or X−ray dose controlled ϕ movement.
The latter one should be used on X−ray sources with variable
X−ray flux (synchrotrons).
________________________________________________________________________
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Table continued from previous page.
_______________________________________________________________________
Item
Description
________________________________________________________________________
First image no.
No. of images
Exp. time
Image number of first image. Range is 1 through 999.
Number of images to be collected. Range is 1 through 999.
Exposure time in seconds. In DOSE mode, the actual time
may be different from the desired exposure time.
Oscillations
Number of ϕ−oscillations per image. One oscillation is
stronlgy recommended for exposure times < 15 min.
∆ ϕ per image
Starting ϕ
ϕ movement per image.
ϕ position to start data collection.
Distance crystal to detector.
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
− TYPE is:
not used
in Single Data Set mode
e.g. /images/zeo_001.mar1200
1, 2, 3 or 4 in Multiple Data Set mode
e.g. /images/zeo_1_001.mar1200
e.g. /images/zeo_INDEX_001.mar1200
e.g. /images/zeo_A_001.mar1200
INDEX
A or B
in Index Crystal mode
in MAD Data mode
− 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 "ϕ increment" (see above).
The starting image will always be 001 and the following images will have numbers that will be
calculated from their ϕ−position relative to image number 001 according to:
XXX = i * ϕ increment / ∆ ϕ + 1
(i=0,1,2,3...)
e.g. with ϕ increment = 90.0 and ∆ ϕ = 2.0, XXX = 1, 46, 91, 136, etc.
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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 to move ϕ very often and that takes time. Finally one ends up with 2 contiguous
data sets A and B, both covering the same ϕ 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:
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 >> and << buttons, respectively.
Note 1:
All changes are saved automatically to file mar345.dat in directory MARLOGDIR and are
available 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!
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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.
One now has the choice of saving
only some sets of programmed
parameters or all of them. By
default, the files to be saved will
be
written
into
directory
$MARLOGDIR/sets. The filename
will always be File_root.set.
To retrieve parameters, press the
"Load"
mar345−Change
window. Select
button
in
Parameters
file by
the
a
double−clicking or by pressing the
"Load" button.
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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. "Starting ϕ" 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 ϕ , 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.
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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
collection
"Go"
really start
"Change"
reedit parameters
"Close"
Close window
During data
collection
"Abort NOW"
Aborts exposure
"Stop AFTER IMAGE"
Stops after current image Close window
Close
________________________________________________________________________
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−ϕ and Image will be updated. The number
of oscillations is given by the multiplier in the ∆ ϕ field. If the scanner is idle, this window
cannot be obtained.
3.9 Stopping Data Collection
Data collection 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 ϕ or distance movement.
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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 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.
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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.
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.
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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
manually 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.
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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 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.
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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
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4.2 Menu Bar
The menu bar features the following buttons:
Windows
Options
Help
Pops up the Windows submenu (see 4.2.1). Shortcut: Alt+w.
Pops up the Options submenu (see 4.2.2). Shortcut: Alt+o.
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.
Shortcut: Ctrl+f
Colors
Close
Pops up the mar345−Colors window.
Shortcut: Ctrl+c
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" was pressed while the 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
Do not/Keep view
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
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
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______________________________________________________________________________________
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.
Available only at zoom factors > 4.
Shortcut: Ctrl+d
Next image
Previous image
Integrate
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 >= 1 only.
Shortcut: Ctrl+i
Zoom options
Pops up a menu with 3 choices that affect the way the image
looks at zoom factors < 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.
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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
Drag
Pops up an empty mar345−Cross section window
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 as follows:
________________________________________________________________________
Button
Action
Result
________________________________________________________________________
Right
Press
Drag
Marks one corner of a zoom area.
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 >= 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.
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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. In the 3D−plot one may rescale the peaks
using the minimum and maximum intensity field on the y−axis of the plot.
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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.
4.4.2 Zoom Buttons
By pressing the full image button, the image will be displayed such that it fits
entirely into the window. The other buttons will zoom in or zoom out.
4.4.3 Colors
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 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.
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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. 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
I <= Min
I >= Max
All other pixel intensities
________________________________________________________________________
Grey scales white
Blue scales black
black
white
red
greys
blues
Rainbow
white
yellow−green−cyan−blue−purple−magenta
________________________________________________________________________
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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). 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.
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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. 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.
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The plot area of the window shows the following features:
Vertical axis
Interpolated intensities
Upper horizontal axis
Lower horizontal axis
Left dashed red line
Length of line in pixel units.
Length of line in mm units.
Marks the begginning of a measured distance. This line can be
moved using the left mouse button.
Right dashed red line
Horizontal red lines
Marks the begginning of a measured distance. This line can be
moved using the right mouse button.
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.
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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. 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/σ ratio!
∆ ϕ per image:
The ∆ ϕ 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 maximum 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!
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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.
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 ϕ 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 opened, 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.
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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.
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
1001
1010
Message: "Error sending command to mar controller"
Reason:
Action:
Network connection to scanner interrupted.
Reboot scanner. Check cables. Try "ping mar345".
Message: "SERVO system cannot be INITIALIZED"
Reason:
Action:
Severe hardware problem.
Call.
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
1030
1040
Message: "Not enough disk space left on device. Aborting data collection"
Reason:
Action:
Disk full.
Clean up disk.
Message: "The Image Plate has been exposed to X−rays"
Reason:
Action:
A running exposure has been aborted.
Erase plate and continue.
Message: "X images 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.
_______________________________________________________________________
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______________________________________________________________________________________
Tabel continued from previous page.
_______________________________________________________________________
No.
Description
_______________________________________________________________________
1050
Message: "SHUTTER did not work properly. Abandoning data collection"
Reason:
Action:
X−ray beam shutter damaged or dirty.
Check shutter. Open and close it manually. Is it very hard
to operate?
1060
Message: "X−ray reading too low ..."
Reason:
Action:
The X−ray intensity as read from the ion. chamber is
below the critical level (see configuration file:
INTENSITY MIN xxx). The data collection starts only
if the X−ray reading is above the configured value.
Check generator, monochromator or collimator.
1061
Message: "X−rays reading too high for DOSE mode ..."
Reason:
Action:
The X−ray intensity as read from the ion. chamber shows
very large numbers (>100). The work in DOSE mode becomes
inaccurate.
Turn down gain selector of ion. chambers.
1070
1080
Message: "Could not recover from previous errors after X retries"
Reason:
Action:
Follow up of previous messages.
Check previous messages.
Message: "SHUTTER did not open during exposure" or
"Shutter did not close at end of exposure"
Reason:
Action:
X−ray beam shutter damaged or dirty.
Check shutter. Open and close it manually. Is it very hard
to operate?
1090
1100
Message: "Scanner home position (X) differs from Y +/− dy"
Reason:
Action:
Problem with radial movement of reading head.
Mail mar.spy. Call.
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.
_______________________________________________________________________
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Tabel continued from previous page.
_______________________________________________________________________
No.
Description
_______________________________________________________________________
1101
1102
1105
Message: "No scan modes found in nb_code ..."
"Something wrong with byteorder in nb_code ..."
"No suitable scanning mode found in nb_code".
Reason:
File $MARTABLEDIR/mar2300.XXX and/or
$MARTABLEDIR/mar3450.XXX may be corrupted or empty.
Check file sizes (73 MB and 103MB). Use command:
catmar $MARTABLEDIR/mar2300.XXX
Action:
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
1111
1112
1115
Message: "Cannot create image file"
"Cannot open image file"
"Error writing image array"
"Error writing image header"
Reason:
Action:
Insufficient disk space or invalid file permissions.
Clean up disk or check data directory permissions.
1215/1241
1234
1238
Message: "Cannot OPEN SHUTTER at START of EXPOSURE"
"SHUTTER was already OPEN at START of EXPOSURE!"
"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:
Action:
Problem with PHI axis movement. Possibly software related.
Mail mar.spy file. Call.
_______________________________________________________________________
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______________________________________________________________________________________
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. 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
! ______________________________________
!
! Only modify the following keywords, if desired...
!
DIST
MIN 75.30 MAX 426.30
!
INTENSITY
MIN 2.0
WARN 20.0
!
USE
SPY
USE
USE
USE
STATS
INCR
RUN
USE
USE
HTML
SUMMARY
!
COLORS
SETS
64
4
!
WAVE
1.541789
Mirrors
Rotating anode
MONOCHROMATOR
GENERATOR
!
NETWORK
!
PORT 4441
HOST 192.0.2.1
MODE 2300
MODE 2000
MODE 1600
MODE 1200
!
ROFF 180 ADC 50 AADD −42 BADD −45
ROFF 180 ADC 50 AADD −42 BADD −45
ROFF 180 ADC 50 AADD −42 BADD −45
ROFF 180 ADC 50 AADD −42 BADD −45
MODE 3450
MODE 3000
MODE 2400
MODE 1800
!
ROFF 180 ADC 50 AADD −42 BADD −45
ROFF 180 ADC 50 AADD −42 BADD −45
ROFF 180 ADC 50 AADD −42 BADD −45
ROFF 180 ADC 50 AADD −42 BADD −45
!IP−Diameter:
!GAPS
345mm
89615
300mm
78601
240mm
63852
180mm
49103
! 02.2.2000: GAPS valid for S/N 120
!
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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 0.15mm (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
==============================================================
4
5
6
7
8
(
(
(
(
(
(
(
(
(
(
(
(
(
192) PROGRAM improve Version 2.8
256) DATE Wed Feb 2 12:00:40 2000
320) SCANNER 120
384) PIXEL
448) PHIOFF
512) CUTOFF
576) SCALE
640) GAIN
704) NUMBER
768) MODE
832) MODE
896) MODE
960) MODE
LENGTH 75 HEIGHT 150 SUBPIXELS 25
269.970
0.000
32767.000
9
10
11
12
13
14
15
16
17
18
19
20
1.000
PIXELS 7766361 NEIGHBOURS 25199739
2300 X
2000 X
1600 X
1200 X
0 Y 1149 ROFF
0 Y 999 ROFF
0 Y 800 ROFF
0 Y 600 ROFF
0 SKIP 144
0 SKIP 144
0 SKIP 809
0 SKIP 809
( 1024) MODE
( 1088) MODE
( 1152) MODE
( 1216) MODE
2300 PIX 7766361
2000 PIX 5956761
1600 PIX 3845618
1200 PIX 2190418
POS 4096
POS 17151502
POS 37076767
POS 52798207
==============================================================
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