George's  8.3.1 Notes

edited 04/10/14

  • Notes on running Delayed Data Collection with BL8.3.1's Robot, Cool Hand Luke

  • View last few entries of luke.log

    Various Notes

    Info on LUKE
    Data Transfer and Archiving

    Click here for James's Notes on "Moving Data Around"

    How to use the "download" command: Example: Firewire on a Mac Computers

                                                   Firewire on Mac using "rsynch" (James's Notes)    

    Firewire  Drives for MS Windows        (or click on link above and scroll down) 

    Restoring Data from a DVD, Local Back up, and other DVD stuff


    Here are a few common problems:
    Please do NOT restart computers or nuke the system without calling beamline James or George !


    Fluorescence Scans in Blu-ICE:
    * Just click on SCAN -> Periodic Table -> the element's edge; The scan's filename, range, step size, and optimization are done automatically.
    * Right click in the view area of the PLOT to see a menu of [file, print, load, plot].
    *Note all scans are printed out after they're done.

    Direct Beam 

    Note that the position of the beam on the detector changes with detector distance.  The data acquisition software takes this into account and updates the coordinates of the beam center written to the header of the image files.  If you want to see what the current mosflm/denzo beam center coordinates are, run  in a terminal window.

    Changing Pinholes and Running  

    The beamline has an active feedback system and is quite stable over time and wavelength changes:  realignment is seldom necessary, unless swapping pinholes.  It should be obvious which pinhole is being used: the 100 micron pinhole will have a beam defining circle of  ~2.5 inches on the touch screen.  The 30 micron pinhole will be ~ 1 inch (and the total flux will be ~15% of the 100 micron pinhole).  To confirm the pinhole size, enter  " grep pinhole /data/log/change.log | tail -1 " in a terminal window.
    Please don't run or change pinholes unless you've been shown how it's done. The instructions below are meant to be reminder of the steps needed to change the pinhole, NOT instructions for people who have not been trained in this (simple) proceedure. Each of the items in green are one of the 8 steps needed to swap the pinholes.
    1. In a teminal window, enter   This will:
      1. move the collimator down
      2. move the goniometer stages to preset positions
      3. wait for you to open the open the hutch door and proceed...
    2. Place the special alignment jig (X-Ray fluorescent YAG crystal with fine hair glued to end) onto the goniometer shaft.  
    3. If you want to change pinholes, and have been shown how, do so now.

    4.  Close the hutch door and press Photons On button.

    5. Press <enter> in the terminal window where you started the script,... then does the following:
      1. The jig will be centered automatically at Low, then High Magnification.
      2. The Divergence will be set to (2.0, 0.35 milli-Rad) and Wave Length (1.1 Angstrom).
      3. will run and optomize the flux.

    6. The beam will then be focused on the YAG, and you will be asked to confirm that the beam defining circle, which will be generated by the computer and displayed on the touch screen, is centered properly. Press <enter> if it looks correct.

    7. The script then determines a new stage-up position for the Collimator so that the beam is on the the Center of Rotation. The user is then asked to confirm that this Center of Rotation is correct and to press <enter>   if it is. If not, the script will iterate from the step, above; otherwise it continues:

      1. is run again with this new stage-up position.
      2. The feedback system is turned on after checking for false spots.
      3. The collimator moves down
      4. the goniometer is moved to its previous position.

    8. carefully remove the alignment jig and place it back in it's vial.

    Stopping and Starting Software
    * At the start (or end) of an indivual user's beamtime, type "finished" to reset the beamline to default conditions.
    * If you need to restart BLU-ICE, kill it by closing the window.  (Also kill adxv and the calculator, since go will start all three running.)
    * Type go to start BLU-ICE, adxv, and a calculator.  (Can also use  dcs,ice, bluice, blu-ice, blue-ice, start, session, ...)
    * To kill and restart ALL data acquisition software, type nuke.  PLEASE DON'T, with out consulting with beamline support staff.


    Scripts For Controlling & Querying The Beamline
    Most scripts are located on  This list and the descriptions are far from complete.
    Look in James's page for all the details, as well as the actual scripts.

    Scripts that control the movement of a motor or actuator can be run with no arguments: the state or the position of that particular device will be returned.  For example:  returns the position of the Vertical Collimator Stage  returns the state of the fast shutter: open or closed  returns the horizontal position of the detector returns the position of the cover: on or off   returns the positon of the beamstop X-Y stage

    ***************sample .com****************** returns the positon of the sample X-Y-Z stage.

    Note: By default moves the sample BY the distance(s) specified. Distances are in Millimeters.  Regardless of goniometer rotation angle,
    +X moves the sample in the beam direction (towards the detector)
    +Y moves the sample down (towards the center of the earth),
    +Z moves the sample away from goniometer, towards cryojet nozzle.

    If only one coordinate is entered it is assumed to be X,
    if two are entered they are assumed to be X and Y.
    Note: there is a space between the command and each coordinate.  X  Y  Z        - moves sample stages by amounts X, Y, and Z 0 .1              - moves sample stage Y by 100 microns. 0 0 -1.0       - moves sample stage Z by minus 1 millimeter.  to X  Y  Z  - moves sample stages to position X, Y, and Z

    If in doubt about relative or absolute moves, you can always use "by" or "to".
    The defaults for and are to move the sample relative, or "by" the amount requested.
    The defaults for and are to move absolute, or "to" the requested position.
    ********************************* Y  - moves the Vertical Collimator to position Y by Y  - moves the vertical collimator by amount Y up - moves stage to the "up" position down  - moves stage to the "down" position
    BEWARE: zero  - sets the current position to be the "up" position X - moves phi to angle X [open/close]  NOTE:  at low MAG (Stage Down) "watchdog.tcl" will CLOSE an open shutter. [on/off] [in/out] [in/out]this is the polarized light source. It's light 2, whose intensity can be adjusted by  [1 or 2,  0-100]which light, what % of full intensity. easy way to send commands to FRONT END computer (look here to get complete list of commands recognized by labVIEW, the control software.) X - sets the photon energy to wavelength X [Horizontal, Vertical]; units are in milli-radians , defalts are 2.00mr X 0.35mr. [active]: - puts in diode, opens shutter, auto-scales then reads I-end, closes shutter, retracts diode (Stage must be UP) (no parameters ) focuses the object in the Hi Mag view (only). - tunes the front-end [keep]  -will turn on feedback (after checking for false spots) -finds the center of rotation of the object in the HIGH MAG view, then calculates how far the Vertical Collimator needs to move in order to have beam center on the rotational axis. -finds the coordinates of the center of the beam on the YAG crystal in view. -moves the object in view (Hi or Low magnification) onto the Center of Rotation -Calculates the time to completion for the current run.  (The script will run until killed or collection stops.  If collection hasn't started in runs and quits)

    Denzo Scripts from 8.2.1           8.3.1 Denzo Site Def from James

    On a linux box, to determine how many images can be stored on the disk,
    for a Q315 use  df --block-size 18M
    for a Q210 use  df --block-size 8M