TiltPicker Usage » History » Revision 18
Revision 17 (Neil Voss, 04/15/2010 09:01 AM) → Revision 18/19 (Neil Voss, 04/15/2010 09:07 AM)
A copy of this page is available at: http://emg.nysbc.org/projects/tiltpicker/wiki/TiltPicker_Usage 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. LAUNCHING 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. 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: ** 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 ---- * 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 ---- * Transfer pick particles ** Pick a single particle in only one image. ** Use transfer or *Xfer picks* button -- this automatically transfers the pick to the ---- * DoG pick particles ** Measure particle size using ruler tool (at top), Use 1X tool, zoom in to get accurate best value ** Sometimes it is best to use a 10% lower estimate for the diameter, e.g., use 30 if you measure 34 ** You can run Run DoG picker with wrong contrast and reject ** Reject picks ** Run DoG picker with correct contrast ** Show terminal ** Accept picks ** If not enough picks were made lower the threshold ** Look at DoG map images ** If the peaks are not crisp dot and more like fuzzy balls, try reducing the particle diameter ---- * 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: ---------------------- Notes: # The underlined letter on the button means that you can use the Alt button (Option on a Mac) and that letter to push the button. # If the button name is followed by three dots '...', it means a pop up window will be displayed for more input. # All buttons are also availale at the top menu (from left to right) * Apply (Alt-A) -- Displays picked particle locations from one image in the other image as circles * Theta... (Alt-T) -- Determine the tilt angle difference between images independent of tilt axis rotation (positive, untilted on left; negative, untilted on right) * Optimize... (Alt-O) -- Perform least squares refinement of all alignment parameters * Mask (Alt-M) -- Hide non-overlapping regions in the images (based on alignment parameters) * Auto Optimize (Alt-Z) -- Automatically perform above 3 steps: Theta, Optimize, and Mask in single click * Rm Worst Picks (Alt-W) -- Remove the worst picks by alignment error highlighted by a yellow plus (+) symbol * Cutoff... (Alt-C) -- Remove the worst picks by specifying an alignment error * Xfer picks (Alt-X) -- Transfer picks from one image to the other based on the alignment parameters * Rm Polygon (Alt-P) -- Remove all points located within a drawn polygon from both images, good for large pieces of crud * Reset... -- Reset all parameters and remove all picks, i.e., start over. * Dog Pick... (Alt-D) -- Run automated particle picker. Requires an estimate of the size of the particle (in pixels) * Quit (Alt-Q) -- Quit the program