Appion » TiltPicker

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h2. RUNNING THE PROGRAM: ======================

To run the program, type:

1. ./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:

1. ./runPicker.sh

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

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h2. BUG TRACKING: ======================

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

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h2. YOUTUBE MOVIE: ======================

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/

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h2. STEP BY STEP TUTORIAL: ======================

TiltPicker Usage

• Start TiltPicker
  o Extract TiltPicker, on command line type:
  tar -zxf tiltpicker-2.0.tgz
  o Go to tiltpicker directory, on command line type:
  cd tiltpicker
  o Display TiltPicker help, on command line type:
  ./ApTiltPicker.py -h
  o Open TiltPicker, on command line type:
  ./ApTiltPicker.py -l data/rawu048b.jpg -r data/rawu049b.jpg -t 50.0

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

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

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