Last modification: 23-Jan-2008
The desktop beamline (dtb) is a highly sophisticated goniometer system. Almost all movements are motorized and can be controlled by a host computer. This allows for a detector system mounted onto the dtb to be aligned with the beam without user intervention. The dtb is capable of finding the beam and refining the optimal position thus yielding the best possible primary X-ray beam intensity. In addition, a beam profile can be obtained and slit apertures can be determined automatically to fit the monochromators properties.
Table 1: dtb hardware components
| Component | Features |
|---|---|
| Goniometer | - High precision PHI-axis - Motorized crystal (PHI-axis) translation - Optional PHI-swing for mounting cooled crystals |
| Collimator | - 2 pairs of hor. and ver. slits followed by ionization chambers - Rotary beam shutter - CCD-microscope with viewing direction along X-ray beam - Motorized beamstop |
| Cardanic cradle | - Positional alignment motors: hor. and ver. translations of entire instrument - Directional alignment motors: hor. and ver. rotations of detector mount coupled to collimator |
| Detector mount | - Vertical 2-theta arm - Crystal-to-detector translation stage |
| Others | - Optional motorized cryo-head translation -Optional automatic cryogenic sample changer ("csc") |
The dtb features an expandable number of high precision stepper motors. Most of the motors are driven by a dedicated motor stepper control module which is an autonomous piece of hardware with its own microprocessor (CPU). The motor modules are coupled to a high speed industrial serial bus (CAN-bus). Each module receives commands and sends status information to the CAN-bus. On the CAN-bus, each member is identified by a unique number or "id" in a similar way as computers in a network. The numbers are arbitrary but must be unique. Note, that the main dtb controller manages the motors for the PHI-axis, the beamstop and the 2 pairs of slits of the collimator. Those motors don't have their own stepper modules.
The main dtb controller is a minicomputer that works as interface between the host computer and the motor modules on the CAN-bus. It features an Ethernet interface to the host-computer and translates commands from the outside world into appropriate signals for the CAN-bus and viceversa. The controller is driven by a real-time operating system and implements the usual TCP/IP-services, i.e. ping, telnet, and ftp. Program mar345dtb communicates with the controller using standard Unix sockets on dedicated ports. In program mar345dtb the motors are usually referenced by certain abbreviations.
Table 2: dtb motors and their names within program mar345dtb
| Name | CAN-id | Description |
|---|---|---|
| SLIT_1_VER | 1 | Vertical slit in front of 1. ionization chamber |
| SLIT_1_HOR | 2 | Horizontal slit in front of 1. ionization chamber |
| SLIT_2_VER | 3 | Vertical slit in front of 2. ionization chamber |
| SLIT_2_HOR | 4 | Horizontal slit in front of 2. ionization chamber |
| BEAMSTOP | 5 | Translation of beamstop along beam |
| PHI | 6 | Phi-axis |
| THETA | 11 | 2-theta arm |
| DISTANCE | 12 | Translation of detector along beam |
| TRANS_VER | 13 | Vertical translation of dtb (up/down) |
| ROT_VER | 14 | Vertical rotation of dtb (up/down). Center of rotation is inbetween 1. and 2. ionization chamber. |
| TRANS_HOR | 15 | Horizontal translation of dtb (left/right). |
| ROT_HOR | 16 | Horizontal rotation of dtb (left/right). Center of rotation is inbetween 1. and 2. ionization chamber. |
| XTAL_Z | 17 | Translates crystal along PHI axis |
| CHI | 18 | Optional Phi-swing: rotation of Phi-axis up to + 90 deg. |
| SERVER | 19 | Sample changer only: mounts sample on goniometer head |
| ROTOR | 20 | Sample changer only: brings sample from carousel close to goniometer |
| LIFTER | 21 | Sample changer only: lifts sample out of carousel |
| PICKER | 22 | Sample changer only: picks a sample in carousel |
| CAROUSEL | 23 | Sample changer only: turns carousel |
| ACTUATOR | 24 | Optional: translation for cryo-head |
| XTAL_X | 26 | Optional: x-translation of crystal on goniometer head |
| XTAL_Y | 27 | Optional: y-translation of crystal on goniometer head |
The geometrical setup of the desktop beamline is such that a beam passing through the collimator will hit a sample mounted on the goniometer. The cross-hair of a CCD-microscope is centered at the intersection of the primary beam with the sample mounted on the PHI-axis. On the detector translation stage an area detector (CCD, Image Plate) is mounted such that at 2-theta=0 the center of the area detector corresponds to the center of diffraction of the sample.
During the "alignment" procedure the desktop beamline drives into a position where the primary X-ray beam passes through the collimation system. To achieve this, 2 motors are required that translate the entire instrument along the beam and 2 motors that rotate the collimator and a frame with the goniometer and detector translation around the beam. The horizontal and vertical axes of rotation are centered at some point close to the first ionization chamber. Within the program the 4 motors are called:
In order to understand how the alignment works it helps to have a look at the design of the collimator. It consists of 2 pairs of continuously variable slits followed by an ionization chamber each. The ionization chambers detect the intensity of the primary X-ray beam coming through the slits. The readings of the ionization chamber within the collimator are obtained by constantly digitizing currents as produced by the X-ray beam. For this purpose, each ionization chamber is coupled to a 16-bit ADC with extremely high sensitivity. The range of operation is from weak sealed-tube sources to 3rd generation synchrotron sources. As is usual for ADC's, there is an offset that marks a baseline of the ADC. This offset is adjustable and must be set such that without X-ray beam the readings don't drop to 0. The stability of the ADC readings depends on temperature and humidity, so varying ambiental conditions will have some influence on the readings. See below for more details about how to adjust the ADC offsets.
The alignment procedure usually consists of the following steps:
The remote control unit features 5 buttons with multiple functionality. The buttons are called "CRYO, BEAMSTOP, THETA, DISTANCE, CHI". For all buttons, 3 states are possible and marked by an LED positioned under the button:
The buttons work the following way:
For DISTANCE the typical situation is that the detector sits close to the crystal and you want to drive it out of the way for crystal mounting. Afterwards, you want to drive the detector back to where it was. For this purpose, position 1 should be handled dynamically and position 2 should be set far away from the crystal, e.g. to 400 mm. I.e. when operating the distance via the remote control will move to 400 mm when pushing the DISTANCE button once or otherwise move back to its original position.
For THETA, position 1 should be at 0.0 degrees. An alternate position should be set to a relatively small value in order to avoid collisions, e.g. 5 degrees. I.e. the dtb is allowed to move in the range 0 and 5 degrees via the remote control.
For CHI, position 1 should be at 0.0 degrees. Position 2 should be set to a comfortable position where to mount a crystal. It is NOT suggested to set it to 90 degrees since here the CHI arm may collide with the cryo cooler. It is safer to stay below 80 degrees!
The CRYO button originally did not have any function, and on some dtbs without
a cryo actuator this button has been reassigned to drive the BEAMSTOP motor.
For instruments delivered before 2004, the
It is possible to reassign buttons of the remote control to take other
functions.
For more details about how to reassign buttons,
to do so, please refer to
chapter 7.2.1.2 (keywords for dtb)
and to
chapter 9.2 (How to Assign Motors to the Buttons of the Local Motor Control)
.
Table 3: Additional buttons on the "M"-version of the remote control unit
The extended version of the remote control unit allows for operation of the
motors used with the optional automatic sample changer. In this setup, the
dtb is extended by motors for the x- and y-movements of the goniometer head
and by those to take sample out of the carousel of the sample changer.
In addition to the buttons in the "M"-version of the remote control unit,
you will find:
Table 4: Additional buttons on the "XL"-version of the remote control unit
mar345dtb is a highly integrated graphical user interface for
collecting data with the mar345 detector mounted on the
desktop beamline. The program is fully menu driven and features
options for setting up one or more data collection runs. It allows
for fully automatic alignment of the instrument with the beam. It also
features an area for image display and analysis.
The program is provided as binary executable for Linux. Due to decreasing
importance of SGI IRIX and Compaq Tru Unix, support for those architectures
is discontinued. The program may run also on Mac OSX, but the TV stream
from the crystal cannot be displayed onto the screen from within the
application. Hence, usage of the program on OSX is not recommended.
Table 5: Supported architectures and operating system versions
Program mar555dtb is a derivative of program mar345dtb.
As far as the goniometer is concerned, it provides the same functionality
as program mar345dtb and hence, the documentation for that
program version is fully valid for program mar555dtb. The
fundamental difference is that program mar555dtb directly interfaces
to the mar555 flatpanel detector instead of the mar345 image
plate detector. While the latter one communicates with the host PC via
TCP/IP-sockets, the mar555 flatpanel detector uses a fiber-optic
high speed link. The data read-out time is small compared to the image
plage (≤ 2 sec). See the documentation of program mar555 to
learn more about the mar555 flatpanel detector.
Whereever appropiate, differences in the GUI between program mar555dtb
and mar345dtb will be pointed out.
Program mar345dtb needs about 100 MB physical RAM, mainly
for transforming incoming images from the detector. Most of the time, however,
the program is not very busy and does not consume too much CPU time.
For image display and other visualization purposes, a 24-bit color display
is mandatory. The program requires a minimum screen resolution of
1280x1024 pixels. The program makes use of large transformation tables,
so the minimum program installation requires a disk space of 200 MB.
Further components in the current mar-software distributions like
the automar-data processing package may increase the required
disk space to 300 MB.
The following specifications are considered as minimum requirements:
Table 6: Computer specifications
2.1.4.2 "M"-Version
The extended version of the remote control unit allows for operation of the
motors used with the optional automatic PHI axis. In this setup, the dtb is
extended by motors for the x- and y-movements of the goniometer head.
The remote control unit allows to drive x,y- and z-translations of the
goniometer head as well as the PHI axis.
Button
Function
X+
Moves crystal to the right if PHI=90 deg.
Moves crystal to the left if PHI=270 deg.
Moves crystal up if PHI=0 deg.
Moves crystal down if PHI=180 deg.
X-
Opposite to X+
Y+
Moves crystal to the right if PHI=0 deg.
Moves crystal to the left if PHI=180 deg.
Moves crystal up if PHI=90 deg.
Moves crystal down if PHI=270 deg.
Y-
Opposite to Y+
Z+
Moves crystal away from PHI-handle
Z-
Moves crystal towards PHI-handle
PHI-X
Moves PHI to either 90 or 270 deg., i.e. a position
where an x-translation moves the crystal either left or right.
PHI-Y
Moves PHI to either 0 or 180 deg., i.e. a position
where an y-translation moves the crystal either left or right.
Magnet
Activates or deactivates the holding magnet on
the goniometer head.
2.1.4.3 "XL"-Version
Button
Function
CAR-
Decreases the current carousel position by 1 unit
CAR+
Increases the current carousel position by 1 unit
INIT
Initializes all sample changer motors including x,y,z-translations of goniometer head
INIT CAR
Initializes the CAROUSEL and LIFTER.
UNLOAD
Unmounts the sample that is currently mounted on the
goniometer head to the selected carousel position.
GIVE/TAKE
GIVE: the vial in the selected carousel
position is taken out of the carousel and presented to the user.
TAKE: a vial is moved from the presentation position into the
carousel position where the GIVE operation has started.
2.2 General Remarks About Program mar345dtb
Architecture
Operating system
Linux PC
SuSE >= 8.0, RedHat >= 8.0
2.3 General Remarks About Program mar555dtb
2.4 Computer Requirements
Component
Requirement
CPU
Intel or AMD > 1 GHz
Memory (RAM)
>= 256 MB
Disk space
>= 4 GB
Mandatory components
1.) Dedicated Ethernet card set to IP-address 192.0.2.2,
twisted pair (10baseT) with RJ-45 connector, 10MB/sec compatible
- 2.) TV-card for capturing signal from crystal camera,
e.g. Hauppauge WinTV
Peripherals (optional)
DVD or CD-writer (ATAPI or SCSI)
Monitor
19'' or larger, 1280x1024 pixels @ > 70 Hz
Graphics card
24 bit colors at 1280x1024 pixels @ > 70 Hz
Required software
X-windows & Motif support
v4l-compontents (video for Linux)
Important notes: