Last modification: 18-Nov-2008
Program mar345dtb uses the following input files. Some of them are mandatory, others optional.
Table 1: mar345dtb input files.
| File type | File name | Mandatory | Description |
|---|---|---|---|
| Configuration | $MARTABLEDIR/config.### | yes | Configuration parameters for dtb and mar345-detector |
| Calibration | $MARTABLEDIR/mar2300.### $MARTABLEDIR/mar3450.### | yes | Calibration files for 150 and 100 micron scan modes (for mar345-detector) |
| Parameter | $MARLOGDIR/dtb.dat | no | Saved parameters from "Edit" |
| Shell script | $MARLOGDIR/dtb.csh | no | Shell script template for executing external commands |
| Command | $MARLOGDIR/dtb.com | no | Parameter file for triggering an action of the dtb or the scanner |
| Images | ... | no | Image files in several formats |
| Carousel data | $MARLOGDIR/csc/CSC.csv | no | Saved parameters from "CSC" |
### denotes a 3-digit serial number and usually is defined as $MAR_SCANNER_NO (or $MAR_DTB_NO if program mar345dtb is used without mar345 support).
While all parameters used within program mar345dtb are set to reasonable defaults, there are quite a number of parameters that are specific for either a particular model of the desktop beamline or the mar345 image plate detector. Therefore, the program must read in a configuration file for proper function. The configuration file is called config.$MAR_SCANNER_NO and resides in directory $MARTABLEDIR. If the configuration file doesn't exist, the program can't be started. The file is a keyworded ASCII-file which may be edited. Keep in mind that many of the parameters can be absolutely critical for hardware functions, so for editing you really have to know what you are doing!
The configuration file is a keyworded ASCII-file in free format. Lines starting with # or ! are treated as comment lines. Almost all keywords and subkeywords can be truncated to 4 characters. A number of keywords are of general program use, other affect the dtb only and others the mar345-detector only:
The following keywords are of general importance to run the program:
There are a number of options that can be turned on (USE) or off (IGNORE):
Default: USE MAR DTB CRYO SPY ERASE XRAY XTAL VIDEO NFS DISK
Default: IGNORE AMPTEK ADC STATS CSC HARDWARE LIGHT
Defines the IP-address to which to talk to either dtb and mar345
and the socket ports. The timeout is a time given in seconds after
which the program automatically closes and reopens the TCP/IP-sockets
to the hardware.
When using the mar555 detector, only USE | IGNORE should be given.
All other arguments are meaningless.
Default: DTB PORT 4451 HOST 192.0.2.3 TIMEOUT 30
Default: MAR PORT 4441 HOST 192.0.2.1 TIMEOUT 30
Alternative: MAR555 USE
Command to use when opening an editor, e.g. for changing the configuration file.
Default: xedit
Command to run html browser for displaying documentation.
Default: konqueror
Command to use to view graphics image formats (jpg).
Default: display (from ImageMagick suite)
Command to use for analyzing a photo for the purpose of automatic
centering.
Default: loopfind
Command to use for assembling several photos taken during crystal
centering into a combined graphics file. This command is called
from the user interface after the last centering step and the
resulting file is automatically shown on the DISPLAY tab.
Default: montagedtb.csh
Command to use to dump video still photos in jpg. The default
is to call shell script marstreamer which again calls a special
version of program streamer out of xawtv-package.
Default: marstreamer
Command arguments to use for program v4lctl from the V4L (video for linux) interface. If
arguments are present, they will be appended to string "v4lctl" and the entire command
will be executed before opening the frame grabber device. Please note,
that v4lctl will only accept one command per call. If you want to
set several parameters via v4lctl, you need to provide several lines
starting with keyword V4L.
Default: no arguments
Settings relevant for the frame grabber output on the "Crystal"-page:
Command to use to convert mar data images into graphical thumbnail images.
Default: mar2thumb (shell script)
Play sound files when issuing warning, errors, etc. The soundfiles
must reside in directory $MARDOCDIR and must be called mar_errorX.wav
(X=1,2,3) and mar_warning.wav. The command to use to actually play
those sound file must be provided here. If it is left empty, this
feature will be ignored.
Default: none
When displaying images, normally only the resolution is shown in Angstroem. In addition (or alternatively) the corresponding 2-theta values may be printed
Default: SHOW RESOLUTION
Number of grey shades for image display.
Default: COLORS 64
Number of retries for recovering a hardware problem.
Default: RETRIES 5
Hardware commands to be optionally executed at program startup. To turn
off, use SKIP, otherwise USE.
Number of data sets to be programmed. Either 15 or 30
Default: SETS 30
<interval> defines the period of time in milliseconds after which
a status file dtb.status or mar.status will be periodically written to
directory $MARLOGDIR. This ASCII files contains some information
about what the scanner and dtb is currently doing. The purpose for
this is to give any other program a chance to exchange information
with the mar hardware. A value of "0" means that no status file
will be written.
Default: STATUS DTB 0 MAR345 0
<interval> defines the period of time in milliseconds after which
an ASCII-formatted command file $MARLOGDIR/dtb.com will be
periodically checked and parsed.
This file may contain commands for either the dtb or the mar345 and
is the interface for external programs to interact with the mar hardware.
A value of "0" means that no dtb.com file will be checked.
If the keyword PORT is supplied
commands are read using exactly
the same syntax from a TCP/IP-socket on port <port>.
In this configuration you may choose to only read from that socket
or to write something back. If keyword WRITE <interval> is
supplied with a positive number, then a status block is sent every
<interval> ms to the socket. The format of the status block
is described
in chapters 10.8
in section
Output).
If a negative value is given for <interval>, then the same
information that goes into both the scanner and dtb spy files is
written to the socket. If the value is 0, then no strings will
be written.
Please note, that it is the client program's responsibility to
read back information from the socket. If the program mar345dtb
sends data to the socket, but the client doesn't read it, the
program is going to freeze within short time.
Default: COMMAND 0 PORT 0 WRITE 0
With this keyword an additional conversion factor can be applied to
convert step units into mm. The hardware doesn't know anything
about mm or degrees and deals only with steps and microsteps.
The values here are supposed to be constant and are rather of
historical importance. Do NOT modify them!
The MAXTIME value only applies to the mar555dtb program version.
The issue is that the mar555 detector can be used with relatively
short exposure times only. The maximum is 60 sec (60000 msec), but usage
of 30 sec or less is strongly recommended. If a positive value in sec
is given for MAXTIME, the program will automatically split an exposure
longer than MAXTIME seconds into shorter ones
by dividing the exposure time by 2 until the resulting exposure time
is < MULTIPLE seconds. If only MAXTIME is > 0, and MULTI has not
been specified, MULTIPLE is set to MAXTIME.
At the same time, the PHI movement for the exposure is divided by 2.
On output, the images will automatically be added and averaged to
give a single image over with the total exposure time and total PHI range
as specified in the GUI. By default, this feature is turned off.
Default: UNITS STEPS 1 SPEED 1 ACCEL 1 TIME 2.5 MAXTIME 0 MULTI 0
The program creates a new version of several log files to be stored
in directory $MARLOGDIR and subdirectories log, spy, lp and beam.
Here you specify how many versions you want to keep. Note, that spy
files can take quite some disk space, but for keeping track of hardware
problems you will want to keep a reasonable number of copies.
After reaching version N, the first log file will be overwritten.
Default: VERSION LOG 99 etc. (all N=99)
Wavelength of X-rays. This number will be written into the
corresponding section of the resulting images.
Default: WAVELENGTH DEFAULT 1.54178 USE INTERN
[x,y]-coordinates for main window and display window at program
startup. The main window has a fixed size. For the display window
also the width and the height can be configured. This allows the
program to be fit to any screen resolution (>=1280x1024 pixels)
and window manager.
Default: Depends on screen resolution and operating system
The following keywords affect the dtb only:
Default values for ADC offset adjustment for ionization chambers 1 and 2.
<off> is the target offset without X-rays and <d> the
tolerance for reaching the target, typically within 10 % of the offset.
For each ionization chamber a gain selector can be set to HIGH for
weak X-ray sources (rotating anode, sealed tube) or to LOW for
synchrotrons. A suitable target offset for HIGH gain is 1000 +/- 20 and
for LOW GAIN is 20 +/- 2. Note, that HIGH gain is roughly 300 times as
sensitive as LOW gain. The VARIANCE for LOW gain (<dlow>) and HIGH gain
(<dhigh>) should reflect the typical fluctuations of the ADC readings
(without beam) and are typically +/- 2 for LOW gain and +/- 20 for HIGH gain.
These values will play a role in the "Find beam" and "Optimize beam"
procedures. They will decide define suitable thresholds for the start and
end of a peak. The program usually expects a peak to be at least
above the ADC <off> + 3*<dhigh> (or 3*<dlow>)
Default: ADC CHAMBER 1 OFFSET 1000 TOLERANCE 20 HIGH VARIANCE LOW 2 HIGH 20
Default: ADC CHAMBER 2 OFFSET 1000 TOLERANCE 20 HIGH VARIANCE LOW 2 HIGH 20
<min> gives the minimum acceptable X-ray reading of chamber 2 during one
exposure. If reading is lower than this, data collection stops
since it will be assumed that the X-rays went away. To turn this off,
enter a negative value. Otherwise, provide a value that is at least
twice as large as the intensity reading of the 2. chamber without
beam. This reading - of course - depends on the selected gain and
the chosen ADC offset. Typically for rotating anode generators running
with an ADC offset of 1000, a MIN value of 2000 should be suitable.
For operation at a synchrotron with low gain settings and an ADC offset
of 20, a MIN value of 30 is suggested.
<warn> gives the allowed variation of X-ray intensity inbetween the
start and the end of one exposure in percent. If
the variation is larger than this, a warning message is issued and
the data collection stops. This is to avoid unnecessary scans if the
X-ray generator fails. To turn this off, enter a very large value
for <warn>.
<dose> is the minimum intensity required to actually start
an exposure when working in DOSE mode. If the intensity is less
than <dose>, the exposure will not even be started but
waits until the X-ray intensity as measured by the ionization chamber
exceeds <dose>.
Default: INTENSITY MIN 2.0 WARNING 50.0 DOSEMIN 0.1
Here we enter the delay in mseconds the shutter takes to actually
be closed and makes exposure times more accurate. This value
has been calibrated in the factory and is specific for a dtb
but usually in the range 20 to 40 msec.
With this keyword an additional conversion factor can be applied to
convert step units into mm. The hardware doesn't know anything
about mm or degrees and deals only with steps and microsteps.
The values here are supposed to be constant and are rather of
historical importance. Do NOT modify them!
Default: UNITS STEPS 1 SPEED 1 ACCEL 1 TIME 2.5
The program creates a new version of several log files to be stored
in directory $MARLOGDIR and subdirectories log, spy, lp, beam and xtal.
Here you specify how many versions you want to keep. Note, that spy
files can take quite some disk space, but for keeping track of hardware
problems you will want to keep a reasonable number of copies.
After reaching version N, the first file (with N=1) will be overwritten.
XTAL only becomes relevant for automatic centering with the sample
changer. N sets the number of sample photos that are kept. This might
be useful only to find out which samples failed to be centered correctly.
With advent of the sample changer (CSC) major work had to be done to
the dtb firmware. Usually the program determines automatically which
dtb firmware version is in use but only if keyword STARTUP VERSION
is given.
Default: VERSION LOG 99 etc. (all N=99)
Wavelength of X-rays. This number will be written into the
corresponding section of the resulting images.
Default: WAVELENGTH DEFAULT 1.54178 USE INTERN
[x,y]-coordinates for main window and display window at program
startup. The main window has a fixed size. For the display window
also the width and the height can be configured. This allows the
program to be fit to any screen resolution (>=1280x1024 pixels)
and window manager.
Default: Depends on screen resolution and operating system
The following keywords affect the dtb only:
Default values for ADC offset adjustment for ionization chambers 1 and 2.
<off> is the target offset without X-rays and <d> the
tolerance for reaching the target, typically within 10 % of the offset.
For each ionization chamber a gain selector can be set to HIGH for
weak X-ray sources (rotating anode, sealed tube) or to LOW for
synchrotrons. A suitable target offset for HIGH gain is 1000 +/- 20 and
for LOW GAIN is 20 +/- 2. Note, that HIGH gain is roughly 300 times as
sensitive as LOW gain. The VARIANCE for LOW gain (<dlow>) and HIGH gain
(<dhigh>) should reflect the typical fluctuations of the ADC readings
(without beam) and are typically +/- 2 for LOW gain and +/- 20 for HIGH gain.
These values will play a role in the "Find beam" and "Optimize beam"
procedures. They will decide define suitable thresholds for the start and
end of a peak. The program usually expects a peak to be at least
above the ADC <off> + 3*<dhigh> (or 3*<dlow>)
Default: ADC CHAMBER 1 OFFSET 1000 TOLERANCE 20 HIGH VARIANCE LOW 2 HIGH 20
Default: ADC CHAMBER 2 OFFSET 1000 TOLERANCE 20 HIGH VARIANCE LOW 2 HIGH 20
<min> gives the minimum acceptable X-ray reading of chamber 2 during one
exposure. If reading is lower than this, data collection stops
since it will be assumed that the X-rays went away. To turn this off,
enter a negative value. Otherwise, provide a value that is at least
twice as large as the intensity reading of the 2. chamber without
beam. This reading - of course - depends on the selected gain and
the chosen ADC offset. Typically for rotating anode generators running
with an ADC offset of 1000, a MIN value of 2000 should be suitable.
For operation at a synchrotron with low gain settings and an ADC offset
of 20, a MIN value of 30 is suggested.
<warn> gives the allowed variation of X-ray intensity inbetween the
start and the end of one exposure in percent. If
the variation is larger than this, a warning message is issued and
the data collection stops. This is to avoid unnecessary scans if the
X-ray generator fails. To turn this off, enter a very large value
for <warn>.
<dose> is the minimum intensity required to actually start
an exposure when working in DOSE mode. If the intensity is less
than <dose>, the exposure will not even be started but
waits until the X-ray intensity as measured by the ionization chamber
exceeds <dose>.
Default: INTENSITY MIN 2.0 WARNING 50.0 DOSEMIN 0.1
Here we enter the delay in mseconds the shutter takes to actually
be closed and makes exposure times more accurate. This value
has been calibrated in the factory and is specific for a dtb
but usually in the range 20 to 40 msec.
Default: SHUTTER 0
Default parameters for the "Find Beam"-procedure of the
automatic alignment. The start and end values for X and Y are given
either as percentages (subkey "%") of the available driving range
(e.g 25 to 75) or in absolute
millimeters (subkey "MM") which would be rather inconvenient.
The 2 values following the SLIT subkey define the aperture of the
horizontal and vertical slits for this procedure.
The method used for doing the beamsearch can be influenced by
subkeywords FAST or SLOW on the OPTIMIZE keyword (see below)!
Default: FIND CHAMBER 1 X 25 75 Y 25 75 % SLIT 3.5 3.5
Default: FIND CHAMBER 2 X 15 85 Y 15 85 % SLIT 3.5 3.5
Default parameters for the "Optimize Beam"-procedure of the
automatic alignment. The speed values for horizontal and vertical
movement are specified separately and are a percentage of the
maximum speed.
The 2 values following the SLIT subkey define the aperture of the
horizontal and vertical slits for this procedure.
The 2 values following the FIRST subkey define the aperture of the
horizontal and vertical slits of chamber 1 used for optimizing
chamber 2. The slit apertures to be used depend on the nature
of the beam. The defaults are appropriate for Osmic mirrors but
should be decreased for a synchrotron beam.
The 2 values for the RANGE subkey define the default range for
horizontal and vertical translation or rotation motors used during
the optimization. The values to be entered are supposed to be
multiples of the used slit size, typically 3 for a beam produces by
a standard generator with standard optics. The range should be
increased for very fine beams on synchtrotrons when using slit sizes
of 0.1 to 0.2 mm.
The FAST or SLOW subkeys define the optimization method. In FAST mode
(available since version 2.2), vertical movements are interrupted as
soon as the instrument moves out of the beam. The decision when beam
is going to be lost is marked by subkey THRESHOLD. If the intensity
drops below <pct> percent of the seen maximum, the movement
is stopped. This speeds up the
optimization and also the beamsearch procedure by a factor of 1.5 to 2.
Default: OPTI CHAMBER 1 SPEED 10 100 SLIT 0.6 0.6 RANGE 3.0 2.0
Default: OPTI CHAMBER 2 SPEED 20 30 SLIT 0.3 0.3 FIRST 0.3 0.3 RANGE 3.0 3.0
Default: OPTI FAST THRESHOLD 75
MOTOR stands for a particular motor and is any of:
The following subkeywords define the specifications of the corresponding motor:
For each motor there are additional keywords to define certain properties:
Use or ignore remote control. Optional keyword CHECK means that the "Remote Control"-window cannot be closed until the remote control is explicitely disabled from the software. This option prevents users from accidentally operating the remote control manually while motors are operated from the software.
Optional keyword MASK specifies which buttons of the remote control unit can be activated at all. This differs from standard dtb's to the ones that come with sample changer. The sample changer requires an extended remote control unit with buttons to move the carousel etc. The mask to use is a bit mask and is either: 131071 for a plain dtb, 16777215 for a dtbcsc with cryo actuator and 16777214 for a dtbcsc without cryo actuator.
The following components are availabe:
Note that as by early 2002 the CRYO button is not being used and may be reassign to drive either the BEAMSTOP or the PHI-motor. It can be handy to drive the beamstop out of the way when mounting the crystal. The beamstop may be moved manually but if this has been done the motor needs to reinitialized afterwards. Alternatively, it can be useful to drive PHI to 0.0 with the remote control before mounting a new crystal. The user can make her/his own choice but the instructions in chapter 9.2 (How to Assign Motors to the Buttons of the Local Motor Control) . must be followed before the keyword given here is going to take effect.
For each components, the following otions are available:
Default: CSC IGNORE NOAUTO NOSHIFT NOINIT_Z BARCODELEN 8
CAP USE MINSHIFT 1 MAXSHIFT 350 CORREL 0.8 ZMAX 3.0
METHOD 0 START 0.0 DPHI 90.0 PHOTOS 4 CYCLES 1 TOLERANCE 0.1
CSV NOPIN BARCODE IDENTIFIER
The following keywords affect the mar345-detector only:
Type of monochromator. This string will be written into the
corresponding section of the resulting images.
Default: MONOCHROMATOR MIRRORS
Type of X-ray source. This string will be written into the
corresponding section of the resulting images.
Default: GENERATOR ROTATING ANODE
Gain for conversion of X-rays into ADC-units for the image plate
detector. These gain factors differ between the 100 micron
and 150 micron scanmodes due to double sampling in the latter one.
The values will be written into the image header and play a role
only later during data processing when it comes to a statistically
correct estimate of the variances of the reflection intensities.
The values provided by marresearch are calibrated and
scanner specific.
Default: GAIN 100u 1.0 150u 0.65
Choice for using a center correction table during transformation.
This implies the existence of files center2300.$MAR_SCANNER_NO
and center3450.$MAR_SCANNER_NO in $MARTABLEDIR. Technically,
from each pixel in a transformed image a calibrated fixed count
is subtracted. By providing
a minimum pixel count, pixels will be forced not to drop below
a given count (default to 5).
Default: CENTER IGNORE MIN 5
Here you specifiy scanner specific values for ADC properties and
radial offset corrections for each scanmode (one of 2300, 2000, 1600,
1200, 3450, 3000, 2400, 1800). In particular the ROFF value is really
scanner specific and is calibrated during the manufacturing process.
The AADD and BADD values are rather dependent on the controller of
the detector and have to do with finding an optimal baseline for
the ADCs used for digitizing the data. Do NEVER EVER change these
values!
The scan command of the mar345-detector may be used
with some special flags used for debugging. The number can be
any hexadecimal combination of the following codes:
The program reads a large calibration file during each scan.
To improve reading efficiency, data are read in in larger blocks.
Only used in program versions < 2.
The scanning head of the mar345-detector is mounted
on a translation stage. During a scan the scanning head
passes a couple of especially marked positions (gap) that
serve as a reference for the correct scanning head positions.
The positions are hardwired and scanner specific. For a
scan at a certain diameter the positions should always stay
the same. The posi tions are given in relative motor
steps. The expected tolerance normally is +/- 5 steps. Larger
variations of the found "gap" positions may indicate a problem
with the scaning head spindle. The observed gaps will be written
into image headers, so those values can be verified. If the "GAP"
keyword is given and the observed gap for a scan at a
certain diameter is not within the tolerance, an
error message will be produced and data collection
stops. Under normal conditions, the GAP keyword
should be left out or the tolerance set to large
values, e.g. 99999.
These values are very ciritical program parameters
concerning timing of data transfer across the network
during scan. <t1> is the timeout in millisec-
onds to wait for new data to come in before looking
again on the network socket after a block of data
has been successfully transformed, <t2> is the time
to wait in the case <t1> is a timeout after a block
of data has been received and transformed before
looking for more incoming data. <t2> is a timeout
that occurs if a previous call with a timeout of
<t1> has not been successful. <t3> is another
timeout that happens only at the end of a scan if
there are still some data missing. Most relevant is
<t1>. However, these parameters are considered
strictly internal and modification will have seri-
ous consequences on overall program preformance.
Default: MODE
Example: FLAG 3 would be a scan with high voltage and laser turned OFF.
Default: FLAG 0
Default: MEMORY 1 MB
Default: GAPS 89600 78600 63900 49100 TOLERANCE 99999
Default: DATA_INTERVAL 3 3 10
The following file listing is a typical configuration file for a mar345-detector mounted on the dtb:
! _____________________________________________________________________________ ! ! Configuration file for mar345 S/N 184 and dtb S/N 010 ! _____________________________________________________________________________ ! ! ============================================================================= ! ============================================================================= ! == == ! == Keywords for general program usage == ! == == ! ============================================================================= ! ============================================================================= ! USE DTB USE SCANNER DTB PORT 4451 HOST 192.0.2.3 TIMEOUT 30 MAR345 PORT 4441 HOST 192.0.2.1 TIMEOUT 30 ! INTENSITY MIN 2000 WARN 20.0 DOSEMIN 2.0 ! USE SPY USE STATS ! USE HTML USE SUMMARY ! COLORS 64 SETS 30 ! BROWSER mozilla MONTAGE montagedtb.csh SOUND play ! V4LCTL -c /dev/video0 setinput Composite1 V4LCTL -c /dev/video0 capture overlay VIDEO USE JPG DEVICE /dev/video0 VIDEO BRIGHTNESS 60 CONTRAST 55 AVERAGE 5 VIDEO WIDTH 768 HEIGHT 576 SCALE 474 474 474 VIDEO ORIGIN 368 285 VIDEO OVERLAY ! THUMBNAIL mar2thumb LOOPFINDER loopfind EDITOR nedit ! ! ! WINDOWS params for Linux:KDE (1280x1024 pixels) ! =============================================== ! 1280x1024 pixels: ! WINDOWS MAIN 1123 0 VIEW 45 0 1070 970 ! ! WINDOWS params for Linux:KDE (1600x1200 pixels) ! =============================================== ! WINDOWS MAIN 1444 0 VIEW 45 0 1392 1174 ! ! WINDOWS params for Linux:GNOME (1280x1024 pixels) ! ================================================ ! WINDOWS MAIN 1122 22 VIEW 15 22 1095 942 ! MONOCHROMATOR Synchrotron GENERATOR Rotating anode ! WAVE DEFAULT 1.000 USE ! ! Log file versions to maintain: ! VERSIONS LOG 99 SPY 99 STATS 10 SCAN 99 TIME 99 PROFILE 99 ! ! ============================================================================= ! ============================================================================= ! == == ! == Keywords affecting dtb only == ! == == ! ============================================================================= ! ============================================================================= ! ! ADC values to start with: ! ADC CHAMBER 1 OFFSET 1000 TOLERANCE 20 HIGH VARIANCE LOW 2 HIGH 20 EDIT ADC CHAMBER 2 OFFSET 1000 TOLERANCE 20 HIGH VARIANCE LOW 2 HIGH 20 EDIT ! ! Initialization commands ! STARTUP USE TIME LOCK VERSION REMOTE STARTUP SKIP ADC SHUTTER HV CYCLE ! ! Shutter close delay in [millisec] ! SHUTTER 25 ! ! Find beam params ! FIND CHAMBER 1 X 25 75 Y 25 75 % SLIT 3.5 3.5 FIND CHAMBER 2 X 15 85 Y 15 85 % SLIT 3.5 3.5 ! ! Optimize beam params ! OPTI CHAMBER 1 SPEED 10 100 SLIT 0.6 0.6 RANGE 2.0 2.0 OPTI CHAMBER 2 SPEED 20 30 SLIT 0.3 0.3 FIRST 0.3 0.3 RANGE 2.0 2.0 OPTI FAST ! ! Scaling factors for all motors: ! UNITS STEPS 1 SPEED 1 ACCEL 1 TIME 2.5 ! ! Slits: Basecon-modul 1-4 (ID = 1-4) ! 1 mm = 200 fsteps ! V = 100 fsteps/sec ! A = 4000 fsteps/s*s ! SLIT FIRST VER STEPS 200 SPEED 100 ACC 4000 TIMEOUT 10 DEF 0.4 ID 1 SLIT FIRST HOR STEPS 200 SPEED 100 ACC 4000 TIMEOUT 10 DEF 0.4 ID 2 SLIT SECOND VER STEPS 200 SPEED 100 ACC 4000 TIMEOUT 10 DEF 0.3 ID 3 SLIT SECOND HOR STEPS 200 SPEED 100 ACC 4000 TIMEOUT 10 DEF 0.3 ID 4 ! SLIT FIRST VER MIN -0.03 MAX 4.0 SPEED 100 ACC 4000 BACK 0.2 SLIT FIRST HOR MIN -0.04 MAX 4.0 SPEED 100 ACC 4000 BACK 0.2 SLIT SECOND VER MIN -0.04 MAX 4.0 SPEED 100 ACC 4000 BACK 0.2 SLIT SECOND HOR MIN -0.07 MAX 4.0 SPEED 100 ACC 4000 BACK 0.2 ! SLIT FIRST HOR INITMIN NOINITMAX HASNOREF ABSOL HASMIN SLIT FIRST VER INITMIN NOINITMAX HASNOREF ABSOL HASMIN SLIT SECOND HOR INITMIN NOINITMAX HASNOREF ABSOL HASMIN SLIT SECOND VER INITMIN NOINITMAX HASNOREF ABSOL HASMIN ! ! Beamstop: Basecon-modul 5 (ID = 5) ! 0.15 mm = 1 fsteps ! 1 mm = 6.666 ! V = 2000 fsteps/sec ! A = 500 fsteps/s*s ! BEAMSTOP STEPS 6.6666666 SPEED 100 ACC 500 ID 5 BEAMSTOP MINVAL 5.0 MAXVAL 45.0 DEFAULT 15.0 BEAMSTOP REFERENCE 18.6 SPEED 50 SLOW 20 ACC 30000 TIMEOUT 20 METHOD 19 BEAMSTOP HASNOMIN HASNOMAX HASREF NOINITMIN NOINITMAX NEGATIVE NOINITAUTO ! ! Phi: Basecon-modul 6 (ID = 6) ! 1 deg = 800 fsteps ! V = 10000 fsteps/sec ! A = 20000 fsteps/s*s ! PHI STEPS 800 SPEED 10000 ACC 20000 BACKLASH -0.5 DEF 0.0 ID 6 PHI REFERENCE -0.125 SPEED 4000 SLOW 200 ACC 20000 TIMEOUT 180 METHOD 20 PHI HASNOMIN HASNOMAX HASREF NOINITMIN NOINITMAX NEGATIVE NOINITAUTO ! ! Theta: CAN-modul 1 (ID = 11) ! 1 mm = 400 fsteps ! V = 2000 fsteps/sec ! A = 1000 fsteps/s*s ! THETA STEPS 400 SPEED 2000 ACC 1000 TIMEOUT 120 ID 11 THETA MINVAL 0.0 MAXVAL 30.0 DEFAULT 0.0 THETA REFERENCE MIN -0.115 MAX 30.0 SPEED 2000 ACC 20000 SLOW 500 THETA HASMIN HASMAX INITMIN NOINITMAX NEGATIVE NOINITAUTO ! ! Distance: CAN-modul 2 (ID = 12) ! 1 mm = 400 fsteps ! V = 4000 fsteps/sec ! A = 4000 fsteps/s*s ! DISTANCE STEPS 400 SPEED 4000 ACC 4000 DEF 400.0 TIMEOUT 120 ID 12 DISTANCE REFERENCE MIN 75.0 MAX 425.6 SPEED 2000 ACC 20000 SLOW 500 DISTANCE HASMIN HASMAX NOINITMIN INITMAX POSITIVE NOINITAUTO ! ! Vertical translation: CAN-modul 3 (ID = 13) ! 1 mm = 20000 fsteps ! V = 800 fsteps/sec ! A = 2000 fsteps/s*s ! TRANS VER STEPS 20000 SPEED 800 ACC 2000 TIMEOUT 333 ID 13 TRANS VER MINVAL -7.5 MAXVAL 7.5 DEFAULT 0.0 TRANS VER REFERENCE MIN -7.80 MAX 7.80 SPEED 800 SLOW 500 ACC 2000 TRANS VER HASMIN HASMAX INITMIN INITMAX POSITIVE NOINITAUTO ! ! Vertical rotation: CAN-modul 4 (ID = 14) ! 1 mm = 2500 fsteps ! V = 4000 fsteps/sec ! A = 2000 fsteps/s*s ! ROTAT VER STEPS 2500 SPEED 3000 ACC 2000 DEF 0.0 TIMEOUT 444 ID 14 ROTAT VER MINVAL -17.0 MAXVAL 35.0 DEFAULT 0.0 ROTAT VER REFERENCE MIN -18.0 MAX 37.00 SPEED 3000 SLOW 500 ACC 10000 ROTAT VER HASMIN HASMAX INITMIN INITMAX POSITIVE NOINITAUTO ! ! Horizontal translation: CAN-modul 5 (ID = 15) ! 1 mm = 1600 fsteps ! V = 4000 fsteps/sec ! A = 10000 fsteps/s*s ! TRANS HOR STEPS 1600 SPEED 4000 ACC 10000 DEF 0.0 TIMEOUT 555 ID 15 TRANS HOR MINVAL -9.8 MAXVAL 9.8 DEFAULT 0.0 TRANS HOR REFERENCE MIN -10.00 MAX 10.00 SPEED 4000 SLOW 500 ACC 10000 TRANS HOR HASMIN HASMAX INITMIN INITMAX POSITIVE NOINITAUTO ! ! Horizontal rotation: CAN-modul 6 (ID = 16) ! 1 mm = 1600 fsteps ! V = 4000 fsteps/sec ! A = 10000 fsteps/s*s ! ROTAT HOR STEPS 1600 SPEED 4000 ACC 10000 DEF 0.0 TIMEOUT 666 ID 16 ROTAT HOR MINVAL -33.0 MAXVAL 33.0 DEFAULT 0.0 ROTAT HOR REFERENCE MIN -34.00 MAX 34.00 SPEED 4000 SLOW 500 ACC 10000 ROTAT HOR HASMIN HASMAX INITMIN INITMAX NEGATIVE NOINITAUTO ! ! Crystal Z-translation: CAN-modul 7 (ID = 17) ! 1 mm = 1600 fsteps ! V = 4000 fsteps/sec ! A = 10000 fsteps/s*s ! CRYSTAL Z STEPS 1600 SPEED 4000 ACC 10000 DEF 0.0 TIMEOUT 777 ID 17 CRYSTAL Z REFERENCE MIN -20.00 MAX 20.00 SPEED 4000 SLOW 500 ACC 20000 CRYSTAL Z HASMIN HASMAX NOINITMIN INITMAX NEGATIVE NOINITAUTO ! ! Chi: CAN-modul 8 (ID = 18) ! 1 deg = 437.5 fsteps ! V = 2000 fsteps/sec ! A = 10000 fsteps/s*s ! CHI USE CHI MAXVAL 90.0 DEFAULT 0.0 BACKLASH 0.5 CHI STEPS 437.5 SPEED 2000 ACC 10000 TIMEOUT 888 ID 18 CHI REFERENCE MIN -0.00 MAX 90.00 SPEED 1000 SLOW 100 ACC 20000 CHI HASMIN HASMAX INITMIN NOINITMAX NEGATIVE NOINITAUTO ! ! ============================================================================ ! Optional additional motors, e.g. for sample changer ... ! ============================================================================ ! ! Crystal x-translation: CAN-modul 9 (ID = 25) ! 1 deg = 20480/360 = 56.888 steps ! 1 mm = R*sin(x) with R=3.0 ! V = 1000 fsteps/sec ! A = 5000 fsteps/s*s ! CRYSTAL X USE CRYSTAL X STEPS 56.888 SPEED 800 ACC 5000 DEF 0.0 BACK 0.0 TIMEOUT 777 ID 26 CRYSTAL X REFERENCE MIN -1.650 MAX 1.300 SPEED 500 SLOW 500 ACC 3000 CRYSTAL X INITMIN INITMAX HASMIN HASMAX NEGATIVE NOINITAUTO CRYSTAL X OFFSET 0.0 ! ! Crystal y-translation: CAN-modul 10 (ID = 26) ! 1 deg = 20480/360 = 56.888 steps ! 1 mm = R*sin(x) with R=3.0 ! V = 1000 fsteps/sec ! A = 5000 fsteps/s*s ! CRYSTAL Y USE CRYSTAL Y STEPS 56.888 SPEED 800 ACC 5000 DEF 0.0 BACK 0.0 TIMEOUT 777 ID 27 CRYSTAL Y REFERENCE MIN -1.801 MAX 1.300 SPEED 500 SLOW 500 ACC 3000 CRYSTAL Y INITMIN INITMAX HASMIN HASMAX POSITIVE NOINITAUTO CRYSTAL Y OFFSET 0.0 ! ! Cryo actuator: CAN-modul 11 (ID = 24) ! 1 mm = 1600 fsteps ! V = 4000 fsteps/sec ! A = 10000 fsteps/s*s ! ACTUATOR USE ACTUATOR STEPS 1600 SPEED 3000 ACC 10000 DEF 0.0 TIMEOUT 888 ID 24 ACTUATOR BACKLASH 0.0 MINVAL 0.0 MAXVAL 24.9 ACTUATOR REFERENCE MIN 0.00 SPEED 3000 SLOW 1500 ACC 10000 ACTUATOR HASMIN HASNOMAX INITMIN NOINITMAX HASNOREF POSITIVE NOINITAUTO ! ! ============================================================================ ! For sample changer only ... ! ============================================================================ ! CSC USE CAP IGNORE BARCODELEN 8 CSC MINSHIFT 1 MAXSHIFT 250 CORREL 0.8 NOSHIFT AUTO CSC METHOD 0 START 0.0 DPHI 90.0 PHOTOS 4 CYCLES 1 ! ! ============================================================================ ! Remote control settings ! ============================================================================ ! REMOTE USE REMOTE MASK 16777215 ! for csc, without actuator use: 16777214 REMOTE ADC ENABLE NOEDIT REMOTE THETA POS1 0.0 POS2 5.0 ENABLE EDIT REMOTE DISTANCE POS1 DYNAMIC POS2 300.0 ENABLE EDIT REMOTE CHI POS1 0.0 POS2 60.0 ENABLE EDIT REMOTE BEAMSTOP POS1 18.0 POS2 45.0 ENABLE EDIT ! ! To enable beamstop on button CRYO run the following commands first: ! dtbcmd 103,1,41,5 ! dtbcmd 103,1,40,100 ! dtbcmd 103,1,39,500 ! dtbcmd 103,1,38,-300 ! dtbcmd 103,1,37,-120 ! These commands need to be given only once and the dtb needs to be rebooted ! afterwards. ! ! ============================================================================= ! WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARN ! ============================================================================= ! ! USE CRYO and USE AMPTEK protect the detector from ! driving into collision. If these keywords are removed while ! the cryo-system INCLUDING cryo-mount (!!!) or AMPTEK are present ! considerable damage to both detector and dtb can be produced. ! ! When setting IGNORE CRYO it is ESSENTIAL to also remove ! the cryo-mount (by removing part of the cryo-stream exhaust). ! ! ============================================================================= ! USE CRYO CRYOPARAM OXFORD IGNORE AMPTEK ! ! ============================================================================= ! ============================================================================= ! == == ! == Keywords affecting mar345 only == ! == == ! ============================================================================= ! ============================================================================= ! GAIN 100U 1.00 150U 0.63 ! ! Never ever change keywords from here on ! MODE 2300 ROFF 120 ADC 50 AADD -42 BADD -42 MODE 2000 ROFF 120 ADC 50 AADD -42 BADD -42 MODE 1600 ROFF 120 ADC 50 AADD -42 BADD -42 MODE 1200 ROFF 120 ADC 50 AADD -42 BADD -42 ! MODE 3450 ROFF 120 ADC 50 AADD -42 BADD -42 MODE 3000 ROFF 120 ADC 50 AADD -42 BADD -42 MODE 2400 ROFF 120 ADC 50 AADD -42 BADD -42 MODE 1800 ROFF 120 ADC 50 AADD -42 BADD -42 ! FLAG 0 ! !IP-Diameter: 345mm 300mm 240mm 180mm !GAPS 89659 78656 63903 49146 (08:49 on 30-Oct-2000) !
If used with a mar345-detector, program mar345dtb requires calibration files. Those calibration files contain flood field correction factors as well as the geometrical information required to transform spiral coordinates into a Cartesian grid system. The file names are:
Program mar345dtb continuously saves parameters whenever they change within the program. When starting the program, the saved parameters are read back so the user always finds the latest changes after quitting a mar345dtb session. The parameter file read at startup is called dtb.dat and resides in directory $MARLOGDIR. If the parameter file doesn't exist, program defaults will be used. The program, however, will always create a new parameter file dtb.dat. The parameter file is a keyworded ASCII-file which may be edited.
Parameter files can be created and loaded from within the program. This is useful when working on a project where you always apply the same set of parameters. The parameter files carry the extension ".set" and may be saved using the "Edit -> Save Parameters ..." menu option in the main window. The parameters can be read back by using the "Edit -> Load Parameters ..." menu option ( also see chapter 6.2 in section Edit).
The keywords used in the parameter file dtb.dat are as follows:
Table 2: Keywords in dtb.dat
| Keyword | Arguments | Example | Description |
|---|---|---|---|
| SET | N USE|SKIP | 9 USE | N is the data set number followed either by string USE or SKIP |
| DIRECTORY | STR | /data | STR is a string with a path name |
| ROOT | STR | xtal | STR is a string with image root name |
| SCANMODE | N | 1200 | N is one of 8 scanmodes, either 1200, 1600, 1800, 2000, 2300, 2400, 3000 or 3450 |
| FORMAT | mar|cbf | mar | Image output format: either "mar" or "cbf" |
| COLLECT | TIME|DOSE | TIME | Exposure mode, either TIME or DOSE |
| BLOCKS | N | 1 | N is the number of PHI-blocks |
| NFRM | N | 50 | N is the number of images per block |
| FFRM | N | 1 | N is the first image number |
| OSCI | N | 1 | N is the number of oscillations |
| DPHI | F | 0.5 | F is the Delta-PHI per image |
| IPHI | F | 0.0 | F is the PHI-increment between images |
| DISTANCE | F | 220.0 | F is the distance detector-to-sample |
| PHI | F | 45.0 | F is the starting PHI angle |
| CHI | F | 0.0 | F is the current CHI angle |
| THETA | F | 0.0 | F is the current 2-theta angle |
| WAVE | F | 1.54178 | F is the current wavelength |
| BEAMSTOP | F | 18.5 | F is the current beamstop position |
| XTAL_Z | F | 0.0 | F is the relative crystal translation |
| SLIT1 | F G | 0.71 0.63 | F and G are hor. and ver. slit apertures for chamber 1 slits |
| SLIT2 | F G | 0.45 0.43 | F and G are hor. and ver. slit apertures for chamber 2 slits |
| ERASE | Erase plate before starting data collection | ||
| PHOTO | Save crystal photo after each image | ||
| THUMBNAIL | Produce thumbnails from data images during data collection | ||
| SPIRAL | Also create raw spiral images during data collection | ||
| OPTIMIZE START | Optimize beam before starting data set | ||
| OPTIMIZE | [-]N IMAGE|HRS|MIN|LOSS | 30 LOSS | Optimize beam during data collection after given time or after N images or after N percent loss of X-ray intensity. A negative sign preceding N indicates this option to become deselected. |
| APPEND | [SET] [VIAL] [BARCODE] | SET BARCODE | Append set and/or vial no. and/or barcode (+identifier) to file root on image creation |
| VIAL | N | 14 | Carousel position to take sample from |
| CENT | NONE|MANUAL|XYZ|AUTO [CONFIRM] [SHIFT] | XYZ CONFIRM | Crystal centering method, XYZ and AUTO may be followed by CONFIRM, XYZ may also be followd by SHIFT |
| COMOPT | [1][+2][+3][+4][+5] | 2+5 | Selection of parameters to pass to shell script dtb.csh |
| COM1/2/3/4/5 | STR | sleep 1 | Custom argument for shell script dtb.csh |
Up to here, the keywords are valid for the "SET" number given on the top. With a new SET keyword, the following keywords will be valid for that new set, so a dtb.dat may contain data for all 30 possible sets and the corresponding entries will be used to update the "Edit"-page. A couple of keywords have to be given only once since they are not related to that page:
| SOURCE | STR | Rotating Anode | STR is the id of the X-ray source as given in the "Header Info"-window |
|---|---|---|---|
| POWER | F G | 50.0 100.0 | F and G are kV and mA settings of X-ray source as given in the "Header Info"-window |
| FILTER | STR | Mirrors | STR is the id of the monochromator as given in the "Header Info"-window |
| CENT | F G | 0.0 0.0 | Deviations of center coordinates as given in the "Header Info"-window |
| TRANSLATIONS | F G | -2.048 -1.888 | Refined beam positions of motors TRANS_HOR and TRANS_VER |
| ROTATIONS | F G | -3.241 1.435 | Refined beam positions of motors ROT_HOR and ROT_VER |
| ADVANCED|SIMPLE | Choice of advanced or standard layout for "Edit..."-window | ||
| CSC | N1 N2 N3 N4 N5 N6 [NO]SHIFT [NO]STORE | 3 2 5 4 4 18 | Values to fill in into the "CSC operation"-fields on the "CSC"-page (Change sample, etc.). |
The following example contains parameters for only 1 data set.
#===================================================== # Date: Mon Feb 18 19:03:08 2002 # Automatically saved by mar345dtb: DO NOT EDIT!!! #===================================================== # ---------------------------------- SET 1 USE DIRECTORY /home/mar345/data/ ROOT xtal SCANMODE 1200 FORMAT mar COLLECT DOSE TIME 10 BLOCKS 1 NFRM 1 FFRM 2 OSCI 1 DPHI 1.000 IPHI 89.000 DISTANCE 350.000 PHI 45.000 CHI -0.000 THETA 0.000 WAVE 1.541790 BEAMSTOP 10.050 XTAL_Z 0.000 SLIT1 0.710 0.630 SLIT2 0.400 0.400 OPTIMIZE START OPTIMIZE -30 images ERASE PHOTO THUMBNAIL # ---------------------------------- # --- Shell commands --- COMOPT 1+5 COM1 COM2 COM3 COM4 # --- Optional Header Info --- SOURCE Rotating Anode POWER 50.00 100.00 FILTER Mirrors POLAR 0.000 CENT 0.0 0.0 REMARK # --- Refined X-ray beam positions --- TRANSLATIONS -2.048 -1.888 ROTATIONS -3.261 -2.508 # --- Edit Data Collection in expert mode --- ADVANCED DATA COLLECTION FEATURES # --- Crystal translation disabled in Edit --- XTAL_Z DISABLED # --- Sample Changer Settings: Change, Load, Unload, Give, Take, Pin --- CSC 1 2 1 2 2 18 SHIFT NOSTORE
Program mar345dtb may be completely driven by external commands, i.e. all relevant settings and push-button actions can be bypassed. The command interface comes into variants:
The TCP/IP-interface becoms active, if the configuration file has a negative argument on keyword COMMAND. A typical value would be "COMMAND -8678", i.e. the program would listen on UNIX port 8678 for connections. The program allows for multiple connections on the same port. The syntax for commands to be accepted via the TCP/IP-port is identical to the dtb.com file, i.e. ASCII strings will be evaluated. In return, the TCP/IP-socket writes ASCII-strings back to the same socket containing status information. The syntax is the same as used in the dtb.status file. The frequency is approx. 1/sec.
Note, that the command interface can be used together with the GUI but bears a considerable risk of unwanted or unforeseen dtb or mar345 activity. It must be stated that usage of the command interface is beyond the responsibility of marresearch and all damage produced by running commands using that command interface are not within our liability!
As stated above, all the syntax of the parameter file is used to modify settings of the data collection parameters, i.e. all parameters belonging to a given "SET" will be used to override the corresponding parameters on the "Edit"-pages. The main difference is that the command file in addition to the (optional) keywords of the data collection parameters requires additional lines that actually provide a command to be executed. This line always starts with keyword COMMAND followed by the following arguments:
Table 3: Arguments for keywords COMMAND in dtb.com
| Arguments | Example | Description |
|---|---|---|
| ERASE | ERASE | Erase the image plate |
| SCAN filename | SCAN /data/lysozyme_001.mar1200 | The filename must follow the mar345dtb conventions. The scanmode and format will be taken from the image extension. |
| CHANGE <mode> | CHANGE 1200 | Change the scanmode to: 1200, 1600, 2000, 2300, 1800, 2400, 3000 or 3450. |
| IPS n1,n2,... | IPS 4,0 | Native controller command for the mar345 image plate. |
| DTB n1,n2,... | DTB 101,0 | Native controller command for the dtb. |
| SHUTTER [OPEN|CLOSE] | SHUTTER CLOSE | Open or closes the shutter (or toggles current state). |
| MOVE <motor> <value> | MOVE PHI 90.0 | Drive <motor> to <value>. The motor must be a string as given in chapter Motors in section Introduction. |
| DEFINE <motor> <value> | DEFINE DISTANCE 250.0 | Define position of <motor> to be <value>. Beware: this command is VERY CRITICAL and should normally not be used. |
| INIT <motor> MIN|MAX|REF | INIT THETA MIN | Initialize <motor> motor at minimum (near end), maximum (far end) or reference. |
| OPTIMIZE [FIRST] [SECOND] | OPTIMIZE | Optimization beam in first and/or second chamber. Omitting FIRST and SECOND means using BOTH. COMMAND OPTIMIZE requires additional parameters to be provided on the OPTIMIZE keyword (see below). |
| FIND [FIRST] [SECOND] | FIND SECOND | Find the beam in first and/or second chamber. COMMAND FIND requires additional parameters to be provided on the FIND keyword (see below). |
| PROFILE [SLIT <h> <v>] [HOR <hor>] [VER <ver>] [PITCH <val>] | PROFILE HOR 1.5 VER 1.5 SLIT 0.1 0.1 PITCH 0.05 | Produce a beam profile covering <hor> mm in HORIZONTAL direction and <ver> mm in VERTICAL direction using slit apertures in chamber 1 of <h> and <v> mm, respectively. The advance per vertical movement will be <valr> mm. If some arguments are missing, the current settings of the GUI will be used. |
| SHAPE [CHAMBER] 1|2 [HOR|VER <val>] [TRUNCATE <t>] [SPEED <per>] | SHAPE 1 HOR 0.9 TRUNCATE 15 SPEED 20 | Produce a beam shape plot for chamber 1 or 2 for the HORIZONTAL or VERTICAL slit, using an aperture for the non-moving slit of <val> mm at a speed of <per> percent . If some arguments are missing, the current settings of the GUI will be used. |
| ADJUST [CHAMBER] 1|2 [WEAK|STRONG] [[OFFSET] <v>] [TOLERANCE <tr>] | ADJUST CHAMBER 1 OFFSET 1000 TOL 10 CHAMBER 2 OFF 1000 TOL 20 | Reset the ADC readings of chambers 1 or 2 to <v> units with a tolerance of <t> units. If some arguments are missing, the current settings of the GUI will be used. |
| COLLECT [<s1>] [<s2>] [<s3>] ... | COLLECT 3 8 24 | Collect data for sets <s1>, <s2>, etc. Please note, that unless the sets are being reprogrammed by the same command file (using the syntax of the dtb.dat file), the current values in the Edit-page of the GUI for the desired set are going to be used. |
| STOP [AFTER IMAGE|SET] [NOW] | STOP AFTER SET | Stop a data collection after finishing current IMAGE or current SET, or stop a motor movement NOW. |
| CONTINUE [AFTER] IMAGE|SET | CONTINUE AFTER IMAGE | Undoes the effect of STOP AFTER IMAGE or STOP AFTER SET. |
| ABORT | ABORT | Immediately stops current activity. |
| QUIT | QUIT | Makes program mar345dtb shutdown. |
| CSC {CHANGE <vial>} | {LOAD <vial>} | UNLOAD {GIVE <vial>} | {TAKE <vial>} | INIT | RESET | {MAGNET ON|OFF} | {SAVE <file>} | {READ <file>} | | CSC LOAD 18 | Sample changer operations as described in chapter CSC Operations in section CSC. The commands CSC SAVE and CSC READ will save or read sample status files, respectively. |
| CRYSTAL FIND |{CENTER [XY] [<x> <y> <z>]} | CRYSTAL CENTER | Triggers a crystal finding or centering procedure as described in chapter Crystal Centering in section Crystal. While FIND works without further options, CENTER may be followed by xyz-coordinates. If they are omitted, the automatic procedure will be tried. |
Program mar345dtb allows to run external commands at certain times during data collection:
The following listing contains a very simple template for file dtb.csh.
#!/bin/csh -f set argc = $#argv set NUM = 2 set cmd = $1 set LOG = ( $MARLOGDIR/dtb.csh.log ) while ( $NUM <= $argc ) set cmd = ( $cmd $argv[$NUM] ) @ NUM++ end # echo "===============================================================" >> $LOG echo "Time: `date`" >> $LOG echo "Command: $cmd" >> $LOG echo "===============================================================" >> $LOG # # Actual command # echo $cmd sleep 2 # exit
mar345dtb autodetects image file formats. The program actually looks at contents of files rather than at file names only. mar345dtb accepts the following image formats:
Table 4: Image formats accepted by mar345dtb
| Format | Usual extension | Description |
|---|---|---|
| mar345 | .marXXXX | Images produced by mar345 detector |
| cbf | .cbfXXXX | Images produced by mar software in CBF format |
| image | .image | Original format of 180mm/300mm scanners |
| pck | .pck | Images of 180mm/300mm scanners, "pck"-compressed. |
| marccd | .mccd or .#### | Images of marCCD detector |
Program mar345dtb continuously saves carousel data whenever they change within the program. When starting the program, the saved parameters are read back so the user always finds the latest changes after quitting a mar345dtb session. The carousel file read at startup and updated during program execution is called $MARLOGDIR/csc/CSC.csv. The format is described in chapter Carousel File in section Output.