Appion » TiltPicker

A copy of this page is available at:

http://emg.nysbc.org/projects/tiltpicker/wiki/TiltPicker_Usage

RUNNING THE PROGRAM:
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To run the program, type:

./ApTiltPicker.py -1 image1.mrc -2 image2.mrc -p tiltpicks.spi

'tiltpicks.spi' is optional. I left an example in the tiltpicker folder. You must run the program in the tiltpicker folder. To run the example type:

./runPicker.sh

If all works the picker will open up and you'll have two images of ribosomes.

BUG TRACKING:
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TiltPicker bugs are now tracked via the AMI redmine server, visit
 http://emg.nysbc.org/projects/tiltpicker/
 to file any bugs

YOUTUBE MOVIE:
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I just made a screen capture video on how to use it. It is available is low resolution on youtube:

http://www.youtube.com/watch?v=cw1osPBY_JM

or you can download the full screen version from the appion.org website:

http://code.google.com/p/appion/downloads/list

I recommend using VLC to watch it:

http://www.videolan.org/vlc/

STEP BY STEP TUTORIAL:
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• Start TiltPicker
  • Extract TiltPicker, on command line type:

    tar -zxf tiltpicker-2.0.tgz

• Go to tiltpicker directory, on command line type:

  cd tiltpicker

• Display TiltPicker help, on command line type:

  ./ApTiltPicker.py -h

• Open TiltPicker, on command line type:

  ./ApTiltPicker.py -l data/rawu048b.jpg -r data/rawu049b.jpg -t 50.0

• Initialize alignment:
  • Maximize window
  • Set correct zoom for images
  • Center the middle bar
  • Pick 5 partcle pairs
  • Save picks to a file
  • Hit the apply button, circles will not match crosses
  • Find theta (tilt angle)
  • Optimize inplane rotations
  • Optimize all parameters
  • Mask region to only look at overlapping regions, overlap is shown on status bar
  • Hit Auto optimize, it performs find theta, optimize angles and mask in a single click
  • If you look at the Terminal it will tell you how many optimization rounds were performed
  • Use transfer picks button, this works but is based on the alignment parameters

• Auto pick particles
  • Measure particle size using ruler tool, zoom in to get best value
  • Run DoG picker with wrong contrast
  • Reject picks
  • Run DoG picker with correct contrast
  • Show terminal
  • Accept picks
  • Look at DoG map images

• Clean up particle picks
  • Use clear bad picks button
  • Use polygon tool
  • Auto optimize
  • Use cutoff button to remove picks below a threshold
  • Add more picks
  • Save and quit