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

Useful command line ".com" Jiffy Scripts

..... 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 More complete selection of James's vast array of scripts. (Warning: Many maybe out of date.)

  • More information about one of the scripts, below, may be available by clicking on the script "name".

  • calculate_atten.comAttenuation Calculator: for lower divergence to reduce the Radiation Dose Rate
    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[10 15 20 30 50 75 100] Change or Get the size of the X-Ray beam on your crystal; Minimum recommended size is 20.
    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.

  • exposure_time.com
    Calculate the best exposure time based on the current, logged, or any other Radiation Dose Rate.
    You'll need to know the maximum dose you can tolerate (#Mega or #Kilo Grays), the expected dose rate (Grays/sec), and the number of frames.
    An exposure time per frame will be calculated.
    Defaults will be suggested based on last on the flux of the last tuneup and any run information that is in the Run_1 BLU-ICE window.
    The script is interactive and defaults will be suggested.
    1) You will be asked it you want to measure and use the current Dose Rate (flux) NOW,
    - OR- the flux at the last tune up,
    - OR - you can enter any other value to use (in Grays per second).

    2) You'll be asked for the maximum Dose you want.
    Expected lifedose of typical protein crystals:
    ---> Native 30000000 (7 zeros)
    ---> MAD 5000000 (6 zeros)
    ---> S SAD 3000000 (6 zeros)
    ---> Br/RNA 1000000 (6 zeros)
    ---> RT 200000 (5 zeros)

    3) finally you'll be asked how many frames will be in the run.

    flux.com
    To measure "active" current X-Ray Flux:
    ............... Stage must be at High Mag
    ............... move sample out out the beam by tapping on TouchScreen
    ............... Enter Command: "flux.com active"
    ............... move sample back by tapping "Undo" button on TouchScreen
    To report FLux after the last "tuneup.com":
    ............... Enter Command: "flux.com last"
    To report Flux after the last "tuneup.com" BEFORE an image taken at some previous time,
    ............... Enter Command: "flux.com /data/mcfuser/my_old_dir/image_name_x_xxxxx.cbf"


    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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