TiltPicker Usage » History » Revision 14
Revision 13 (Neil Voss, 04/15/2010 08:38 AM) → Revision 14/19 (Neil Voss, 04/15/2010 08:46 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: ---------------------- * 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 ---- * Initialize picking: alignment: ** Maximize window ** Set correct zoom for images, if necessary images ** Center the middle bar, if necessary bar ** Manually pick Pick 5 partcle pairs from each image ** Save picks to a file, file will then auto-save all subsequent picks ---- * Initialize alignment: ** Hit the *Apply* apply button, circles will NOT match crosses ** Find theta (tilt angle) *** -- Hit *Theta...* button *** button, Hit *Run* *** This number should match the value from Goniometer *** *Run*, 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 *** rotations -- Hit *Optimize...* *** *Optimize...*, Hit *Run* a few times *** 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 last 3 steps in a single click ** If you look at the Terminal, Terminal it will tell you how many optimization rounds were performed ---- * Transfer pick particles ** Pick a single particle in only one image. ** Use transfer or *Xfer picks* button -- picks button, this automatically transfers works but is based on the pick to the ---- alignment parameters * DoG Auto 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 ---- * 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: ---------------------- (from left to right)