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TiltPicker Usage » History » Revision 8

Revision 7 (Neil Voss, 04/15/2010 08:29 AM) → Revision 8/19 (Neil Voss, 04/15/2010 08:32 AM)

 
 A copy of this page is available at: 

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

 h2. RUNNING THE PROGRAM: 
 ---------------------- 

 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: 
 ---------------------- 

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


 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/ 


 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 

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

 

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

 

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