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TiltPicker Usage » History » Version 9

Neil Voss, 04/15/2010 08:32 AM

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A copy of this page is available at:
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  http://emg.nysbc.org/projects/tiltpicker/wiki/TiltPicker_Usage
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h2. RUNNING THE PROGRAM:
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To run the program, type:
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  ./ApTiltPicker.py -1 image1.mrc -2 image2.mrc -p tiltpicks.spi
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'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:
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  ./runPicker.sh
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If all works the picker will open up and you'll have two images of ribosomes.
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h2. BUG TRACKING:
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 TiltPicker bugs are now tracked via the AMI redmine server, visit
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 http://emg.nysbc.org/projects/tiltpicker/
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 to file any bugs
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h2. 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:
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 http://www.youtube.com/watch?v=cw1osPBY_JM
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or you can download the full screen version from the appion.org website:
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 http://code.google.com/p/appion/downloads/list
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I recommend using VLC to watch it:
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 http://www.videolan.org/vlc/
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h2. STEP BY STEP TUTORIAL:
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* Start TiltPicker
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** Extract TiltPicker, on command line type:	
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 tar -zxf tiltpicker-2.0.tgz
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** Go to tiltpicker directory, on command line type:
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 cd tiltpicker	
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** Display TiltPicker help, on command line type:
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 ./ApTiltPicker.py -h
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** Open TiltPicker, on command line type:	
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 ./ApTiltPicker.py -l data/rawu048b.jpg -r data/rawu049b.jpg -t 50.0	
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* Initialize alignment:
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** Maximize window
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** Set correct zoom for images
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** Center the middle bar
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** Pick 5 partcle pairs
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** Save picks to a file
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** Hit the apply button, circles will not match crosses
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** Find theta (tilt angle)
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** Optimize inplane rotations
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** Optimize all parameters
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** Mask region to only look at overlapping regions, overlap is shown on status bar
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** Hit Auto optimize, it performs find theta, optimize angles and mask in a single click
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** If you look at the Terminal it will tell you how many optimization rounds were performed
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** Use transfer picks button, this works but is based on the alignment parameters
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* Auto pick particles
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** Measure particle size using ruler tool, zoom in to get best value
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** Run DoG picker with wrong contrast
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** Reject picks
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** Run DoG picker with correct contrast
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** Show terminal
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** Accept picks
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** Look at DoG map images
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* Clean up particle picks	
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** Use clear bad picks button	
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** Use polygon tool
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** Auto optimize
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** Use cutoff button to remove picks below a threshold
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** Add more picks
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** Save and quit