Appion » TiltPicker

A copy of this page is available at:

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

h2. 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.

h2. 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

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:

 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/

h2. 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	

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* Initialize picking:

** Maximize window

** Set correct zoom for images, if necessary

** Center the middle bar, if necessary

** Manually pick 5 partcle pairs from each image

** Save picks to a file, file will then auto-save all subsequent picks

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* Initialize alignment:

** Hit the *Apply* button, circles will NOT match crosses

** Find theta (tilt angle)

*** Hit *Theta...* button

*** Hit *Run*

*** This number should match the value from Goniometer

*** Hit *Apply* to accept this value

** Optimize inplane rotation angles and shift

*** *Refine* means this parameter will be optimized

*** *Lock* means this parameter is locked and will NOT be optimized

*** Hit *Optimize...*

*** Hit *Run* a few times

*** Hit *Apply*

** Use *Mask* button to only look at overlapping regions, overlap % is shown on status bar

** Hit *Auto Optimize*, it automatically performs theta, optimize, and mask in a single click

** If you look at the Terminal, it will tell you how many optimization rounds were performed

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* Transfer pick particles

** Pick a single particle in only one image.

** Use transfer or *Xfer picks* button -- this automatically transfers the pick to the 

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* DoG 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

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* 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

h2. BUTTON DOCUMENTATION:

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(from left to right)