TiltPicker Usage » History » Revision 4
Revision 3 (Neil Voss, 04/15/2010 08:27 AM) → Revision 4/19 (Neil Voss, 04/15/2010 08:28 AM)
====================== 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 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