Data COLLECTION notes are here.
Data PROCESSING notes are here.

A Few Useful Scripts (Under construction...)

..... Almost all of the BL8.3.1 scripts or "jiffy's" end in ".com".
The .com file name extension is a hold-over from the days of DOS and DEC and has no relation to the .com (for "commercial") top-level Internet domain name.

  • See the Holton Untilites for a Much, Much More complete selection of James's vast array of scripts. (Warning: Some maybe out of date.)


  • To get more information about one of the scripts, below. Click on the script "name".

  • deice_buddy.com Park the hutch and get the Goniometer rotating to facilitate Crystal De-Icing with liquid N2 Spray.
    divergence.com Open, Close, or Get current settings of Beam Defining slits.
    exposure_time.com Calculate the best exposure time based on current or calculated Radiation Dose Rate
    flux.com Find the X-Ray Beam Flux and Radiation Dose rate.
    index Index the last image taken and try to get a data collection stratagy
    pinhole.com Change or Get the current Pinhole size of the beam.
    pinlength.com Get or Set the goniometer Z-motor position in terms of a sample's pin length
    process_xds.com Set up Processing of a data set with XDS.
    sample.com Translate your Crystal on the Goniometer, Get the current X Y Z Positions of the corresponding Goniometer motors.
    snap.com Take a picture of your sample
    tuneup.com Maximize the beam intensity
    waypoint_setup.comQuasi-Vector Scan: setup data collection at a series of different points along a crystal.

  • Details, below. Click on the script "name" to see the text of the script itself.

  • deice_buddy.com
    will park the hutch and start the goniometer turning.
    Just close the hutch door to stop the script, or press "Control" and type "c"



    index


    pinhole.com


    pinlength.com


    process_xds.com


    sample.com
    report or change the crystal position.  All distances are in millimeters.
    usage: sample.com [x y z]
    where:
    x   is the distance to move in the direction of the x-ray beam
    y   is the distance to move in the direction of gravity (down)
    z   is the distance to move in the spindle direction (right-hand-rule)
    or:   sample.com to [x y z]
    to  implies that (x,y,z) is an absolute positon of the three sample motors
    x   is the desired position of the first sample motor
    y   is the desired position of the second sample motor
    z   is the desired position of the third sample motor
    example: sample.com
    returns: sample motors are now -0.623 -0.357 2.088
    example: sample.com 0 0.1 0
    returns: sample motors are now -0.722 -0.373 2.088
    example: sample.com to -0.623 -0.357 2.088
    returns: sample motors are now -0.623 -0.357 2.088
    Note in the second example that the relative move "down" by 100 microns changed both the x and y motors.  This is because relative moves are done in the lab frame (x-ray beam, gravity, and spindle axis) and the motor moves are calculated with the current value of phi rotation in mind.  This way, you can use the x coordinate to focus the sample in the mircoscope. 

    snap.com
    will grab a jpeg image from the Axis video server.  This is a core utility for all the automated image interpretation programs, but users will also often want to take a picture of their crystal if it is a particularly pretty one.  This is how you do it.
    usage: snap.com [filename.jpg] [camera] [352x240] [-mark] [-nodisplay]
    where:
    filename.jpg is the name of the image to safe [default: inherited from snapshot run]
    camera       is the axis camera number to use [default: 1]
    352x240      is the desired pixel dimensions of the image [default: 704x480]
    -mark        will draw a circle indicating the beam profile on the image
    -nodisplay   do not display the image after capturing it [default: display it]
    example: snap.com pretty.jpg -mark
    will save the current high-mag camera (#1) video image as "pretty.jpg", mark it with a circle, and display it.
    example: snap.com hutch.jpg 4 -nodisplay
    will save the current image from the overhead camera (in 8.3.1) to the file "hutch.jpg", but will not display it.


    tuneup.com is a full optimization of the x-ray beam through the pinhole. This procedure will move the sample 1mm down the cryostream (to protect it and to get it out of the way). Disable the feedback system. Insert the photodiode. Open the shutter. Maximize the flux out of the monochromator. Maximize the flux through the pinhole with a vertical and horizontal scan of the beam. Then the shutter is closed, diode removed and the feedback system recalibrated to the new beam position. Finally, the original sample position is restored. The hill-climbing features of the frontend software are used first, and then a "manual" scan through the current position is fitted to a parabola in gnuplot.

    waypoint_setup.com
    You must FIRST set up a "Run_1" in the bluice data collection tab before calling this script, then ... This script will create a copy-and-paste text (which you can then execute) to collect sets of images from different locations along your crystal; you will specify the starting and ending points AND the number of points. You can choose to set it up as a single continuous (Run_1) of frames (divided up and) collected at the different positions or, Muliple complete runs at different locations with identical parameters and incremented RUN numbers


  • run "cellvolume.com" from the command line to determine if you have a detectable signal for flurescence scans (>~10 mMolar is required)



  • Calculate the slit postition to achive a desired Attenuation of the Beam to reduce the Radiation Dose Rate
    run "calculate_atten.com" from the command line
    This calculates the horizontal divergence (divergence.com x) needed to obtain a given percentage
    based on 100% full beam (2.0 milliradians; divergence.com 2.0)

































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