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TiltPicker Usage » History » Revision 3

Revision 2 (Neil Voss, 03/17/2010 11:21 AM) → Revision 3/19 (Neil Voss, 04/15/2010 08:27 AM) 

====================== 
 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. 

 ====================== 
 BUG TRACKING: 
 ====================== 

  h1. TiltPicker bugs are now tracked via the AMI redmine server, visit 
  http://emg.nysbc.org/projects/tiltpicker/ 
  to file any bugs Usage 

 ====================== 
 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/ 

 ====================== 
 STEP BY STEP TUTORIAL: 
 ====================== 

 TiltPicker Usage 

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

     
 </pre> 

 * 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