Information about the CrystalLogic Microdiffractometer
R.
Sweet
31 Dec 2007
The adjustable aperture is the same as on the other Crystal Logic diffractometers, rotating "fork" arrangements. Full open is 2mm. The guard aperture also is replaceable pins with fixed apertures in them. The catch here is that to handle microcrystals, the apertures need to be put in place very carefully. Each has its own "best" orientation, which should be indicated by a mark that should be kept at the top. They should be handled only with the special tool, and should be installed with gentle pressure and slight back/forth rotation. This should assure 5-10 micron reproducibility. Get someone to demonstrate to you before you try it yourself. These pins are different from the other diffractometers -- they are tapered to give more accurate fit.
There is a
crystal-alignment microscope that views straight into the incident
x-ray beam. Users may control it from a web-based screen that
provides most useful operations:
http://x25-h.nsls.bnl.gov/axisvid/tryf.html.
(This is accessible only inside the PXRR network firewall.)
Note: The
screen is always live, waiting to Center on your Click; don't click
unless you know what you're doing. There are five primitive
motions for the microscope, plus two more functions. The
primitive motions are vertical (Up Periscope), horizontal
perpendicular to the beam, and horiz. parallel to the beam, then
there is motorized focus and zoom. The zoom is VERY broad,
16X. All of these five motors can be "homed" [ say
how ]. In addition there is a phosphor that can be swung up
into position for viewing of the direct beam, and the illumination
can be controlled.
Grid: there are Display/Hide buttons
at the bottom. This display contains the crosshair to which
objects will be centered after clicks on the screen and grid marks
along each hairline.
Zoom: The top row of buttons on the
screen perform obvious functions, employing the motorized zoom of the
'scope. The Zoom in/out buttons change the scale by about a
factor of 1.3. The grid is required to understand the
magnification, and the scale of this grid is given to the right of
the image in "microns per tick." The range is from
about 135 to about 9 microns per tick. The image will not, in
general, remain in perfect focus over the zoom range. Live with
it for now.
Focus: During setup, the microscope should be
focused on the phosphor -- this will employ the internal optical
focus motor of the microscope. To focus on the crystal, the
software uses the parallel-motion motor to keep the 'scope focused on
the phosphor. The Focus +/- buttons have been scaled to the
zoom level so that individual clicks will be in a range to give
reasonably sharp focus with one click. Note:
the Crystal/Phosphor buttons are
toggled automatically by the Phosphor In/Out buttons, see
below.
Lamp: There are two LED illuminators, above and
below the 45-degree mirror. The upper illuminator is occluded
partly by the top edge of the mirror and mostly illuminates the
collimator block. The lower one illuminates both the crystal
and the background. One at a time, they can be turned off or to
maximum intensity, or can be brightened or dimmed in about three
increments.
Periscope Drive: The Up Periscope button brings
the visualizer into position to view the x-tal. Note:
The beamstop occupies the same volume
as the periscope mirror. The beamstop must be removed by hand
before the periscope is raised. There is no interlock for
this. This command uses the vertical motor only, bringing it to
the last-used vertical and horizontal position, zoom, and focus.
Down Periscope simply puts it away.
The +/- 90 buttons
refer to incrementing the omega axis, which should move at a pace of
about one second per 180 degrees of motion.
Sample motion: The
U/D/L/R and Load / Unload buttons don't work yet.
Phosphor
control: The phosphor is driven up into position by the
buttons. Two other operations are linked to this.
Firstly, the focus is toggled to the phosphor (internal focus motor)
or crystal (parallel-to-the-beam focus motion), depending whether the
phosphor is in or out. Secondly, the crystal is moved down and
away, parallel to the cold stream, before the phosphor is raised into
position, then it is moved back when the phosphor is taken out. Keep
track of what you're doing here. If you rotate the spindle the x-tal
may move out of the beam, although the software does keep track of
the original centered position.
Click-To-Center (C2C):
Below the image are three buttons. The action of all three
buttons is scaled to the zoom level. If something seems odd,
consider re-"homing" the zoom and focus. In any event,
because the zoom is a continuous motion, the motions will not be
precisely accurate. One may require a couple of C2C cycles to get it
right.
Crystal on
Omega -- is "standard" C2C wherein the sample XYZ are
used to attempt to center the specimen on the spindle (Omega) axis.
In general, click on the specimen and it will move to the +-hair.
Click +90. Click specimen again, and you should be done.
Check this by clicking +90 again. If it doesn't seem to work
correctly, check that the spindle axis is on the crosshair -- see
below.
Crosshair to Beam -- Use this in the initial
setup. With the 'scope at lowest zoom one may visualize the
opening of the guard aperture. Use this option to C2C on this
aperture. This is the option that provides precise centering
of micro crystals on the beam. 1. put in phosphor and open
shutter. 2. use crosshair-to-beam to center on the beam. 3.
extinguish the beam and remove the phosphor. 4. execute the
command described next.
Spindle to Crosshair -- this moves
only the sample Z axis and the Omega vertical axis to move the
clicked point to the crosshair. If the crystal has already
been centered on the spindle, this will place its center of rotation
on the beam. A second use is to adjust the vertical position of the
omega axis to the 'scope crosshair. Note the specimen position at
two spindle rotations that are 180 deg apart. Then click at
the center point between the two, on the vertical crosshair,
to bring omega to the same height as the periscope.
Alignment Checklist -- Draft
For crude alignment, homing the slits will open them to full aperture, 2mm. At minimum zoom, pre-align the periscope to have the crosshair aligned to the guard aperture (Crosshair to Beam). Remove the guard aperture. Insert the phosphor on the periscope. Open the shutter.
There are CBASS tweak commands for diffractometer Horiz, Vert. Use them to center the beam on the position of the guard aperture. Note: The lift table AND the vetical axis of the omega drive will follow the optics for all of these motions.
Close down the apertures a ways, then use the CBASS Align button to do simple H/V alignment of the diff'to to the beam.
Use CBASS command-line instruction [ ??? ] to perform pitch/yaw. Again, the lift table will follow these pitch/yaw motions to keep the detector centerline parallel to the collimator axis.
28 Dec 2007
Centering the direct beam on the detector
There is a CBASS command-line instruction that will calculate the motions to make to the upstream and downstream detector-table motions to put the direct beam at the center of the detector for all positions of the detector on the lift table:
bc_calcs v1 h1 D1 v2 h2 D2
Here v and h are the vertical and horizontal distances in mm, to the right and upwards, respectively, of the direct beam from the physical beam centers. D is the specimen-to-detector distance in mm. Measurements should be made at two different distances along the detector table. The result will be written to the CBASS log file [what's the name, John?]. The result will include the increment to move the TZU (upstream vertical table motors tzo and tzi), TZD (the single downstream vert. motor), TYU and TYD (up- and downstream Y motors). If this proves to be reliable, we'll simply bump the motors automatically from CBASS, maybe after a query to the user and confirmation.
The equations that provide this correction are these:
a = (h2-h1) / (D2-D1) b = h1 – a D1
c = (v2-v1) / (D2-D1) d = v1 – c D1
delTYU = - 930 a -b
delTYD = -1570 a – b
delTZU = 630 c + d
delTZD = 1730 c + d
[Other things we need: names of hosts and directory paths for control codes at X25. Who is the owner, pxuser or pxsys? Where is the python? Where are the EPICS codes? What are names of the .db files with the codes that are being used?
28 Dec 2007
John Skinner's notes on locations of
software, etc.
The name of the cbass logfile is
"cbass_outfile.txt". It is really just debug info, and the
output of bc_calcs is just being sent there temporarily until it's
decided how/when/by who that utility will be run.
$CBHOME is
where the Python files that make up CBASS are. It's owned by pxsys,
and should never be edited by anyone but me. It would be unusual for
anyone to look at that code.
$CONFIGDIR/cbass_macros.py holds
the beamline-specific Python code. It's owned by pxuser. It is fairly
readable and can be tweaked by anyone with the confidence to do so.
Typing "reload_macros" in the command-line of CBASS reloads
any changes without the need to exit CBASS.
$CONFIGDIR/epx.db
has the names of the epics motors that CBASS needs to control.
Owned by pxuser. When editing, just be sure to conform to the
existing syntax. "#" does not indicate a
comment!
$CONFIGDIR/epx_monitor.db has the names of the epics
motors that CBASS monitors for live updates. Same rules as for
epx.db.
~/epx_setup holds medms. They have somewhat
descriptive names. [What are the names of useful MEDM
programs?]
~/x25_diffmedms holds additional medms on
x25
/tftpboot/epics/[beamline]-v/db has the epics .db files.
Only Dieter, Chris, and myself mess with these. They're owned by
epics.
The
new Crystal Logic Microdiffractometer in the X25 hutch. 10 Dec 07
The Cartesian crystal orienter on the 8"-diameter servo motor with air bearing will provide sub-micron crystal orientation. There is a kappa-axis crystal orienter to sit atop the crystal orienter.
Detector:
The detector sits on its own translator, isolated from the
diffractometer. Sufficient motions are built into the lift table and
detector carriage that the specimen-to-detector distance can have a
wide range of values and the direct-beam position should remain at a
fixed point.
29. Nov. 2007
To gain control of the Compumotor controller through a serial line from a linux machine:
Plug serial line between the two devices.
Having logged in as pxuser (or maybe root) do --
# minicom ttyS0 (maybe a different port)
To exit minicom: ^a z (menu) x yes
One can cycle power to get a parker compumotor acknowledgement.
Eventually one needs to do >minit to initializethe minicom connection.
Compumotor commands
cdone (says cmd_done) when it's finished.
To KILL a motion: !k
gome = get omega
zeroo = zero omega
Illuminator:
LxMAX - full brightness: Where x =A or B.
LxMIN - turn off
LxUP - turn up 1/32 of range
LxDN - turn down 1/32
Phosphor:
OUTXXX0 - Store phosphor
OUTXXX1 - Place phosphor in beam
Sec. Shutter:
OUTXX0 - open secondary shutter
OUTXX1 - close secondary shutter
Half slits:
1.OUT.9-0 - block outboard side
1.OUT.9-1 - unblock outboard
1.OUT.10-0 - block bottom
1.OUT.10-1 - unblock bottom
Omega Z-motion control:
VAR80=0.5 - set Omega Z for .5mm relative move
MZOM - move Omega Z
GZOM - get Omega Z position
ZROZOM - Zero Omega Z
Optical rail Z-motion control:
VAR81=0.5 - set Optics Z for .5mm relative move
MZOP - move Optics
GZOP - get Optics Z position
ZROZOP - Zero Optics Z
Beamstop motion:
VAR82=0.5 - set Beamstop Z for .5mm relative move
MBMZ - move Beamstop Z
GBMZ
VAR83 for Beamstop X
etc.
Detector distance:
VAR13=0.5 -- Detector distance
MDIST
GDIST
ZEROD
Omega axis rotation:
VAR12 for Omega, MOME
GOME
ZEROO
Other tricks:
LIMLVL to get limit switch activation. In each set of three the first two are limits, the third is home. Probably one gets 0 if the sensor is between limits, then 1/0 for home, depending whether the sensor is blocked.
TLIM does something else with these switches, perhaps showing their actual sense, blocked or open.
