TiltPicker Usage » History » Version 4
Neil Voss, 04/15/2010 08:28 AM
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| 2 | 4 | Neil Voss | h2. RUNNING THE PROGRAM: |
| 3 | 3 | Neil Voss | ====================== |
| 4 | 1 | Neil Voss | |
| 5 | 3 | Neil Voss | To run the program, type: |
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| 7 | 3 | Neil Voss | # ./ApTiltPicker.py -1 image1.mrc -2 image2.mrc -p tiltpicks.spi |
| 8 | 1 | Neil Voss | |
| 9 | 3 | Neil Voss | '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: |
| 10 | 1 | Neil Voss | |
| 11 | 3 | Neil Voss | # ./runPicker.sh |
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| 13 | If all works the picker will open up and you'll have two images of ribosomes. |
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| 15 | ====================== |
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| 16 | 4 | Neil Voss | h2. BUG TRACKING: |
| 17 | 3 | Neil Voss | ====================== |
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| 19 | TiltPicker bugs are now tracked via the AMI redmine server, visit |
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| 20 | http://emg.nysbc.org/projects/tiltpicker/ |
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| 21 | to file any bugs |
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| 23 | ====================== |
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| 24 | 4 | Neil Voss | h2. YOUTUBE MOVIE: |
| 25 | 3 | Neil Voss | ====================== |
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| 27 | I just made a screen capture video on how to use it. It is available is low resolution on youtube: |
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| 29 | http://www.youtube.com/watch?v=cw1osPBY_JM |
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| 30 | |||
| 31 | or you can download the full screen version from the appion.org website: |
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| 33 | http://code.google.com/p/appion/downloads/list |
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| 34 | |||
| 35 | I recommend using VLC to watch it: |
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| 37 | http://www.videolan.org/vlc/ |
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| 38 | |||
| 39 | ====================== |
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| 40 | 4 | Neil Voss | h2. STEP BY STEP TUTORIAL: |
| 41 | 3 | Neil Voss | ====================== |
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| 43 | TiltPicker Usage |
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| 44 | |||
| 45 | * Start TiltPicker |
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| 46 | o Extract TiltPicker, on command line type: |
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| 47 | tar -zxf tiltpicker-2.0.tgz |
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| 48 | o Go to tiltpicker directory, on command line type: |
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| 49 | cd tiltpicker |
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| 50 | o Display TiltPicker help, on command line type: |
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| 51 | ./ApTiltPicker.py -h |
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| 52 | o Open TiltPicker, on command line type: |
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| 53 | ./ApTiltPicker.py -l data/rawu048b.jpg -r data/rawu049b.jpg -t 50.0 |
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| 54 | |||
| 55 | * Initialize alignment: |
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| 56 | o Maximize window |
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| 57 | o Set correct zoom for images |
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| 58 | o Center the middle bar |
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| 59 | o Pick 5 partcle pairs |
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| 60 | o Save picks to a file |
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| 61 | o Hit the apply button, circles will not match crosses |
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| 62 | o Find theta (tilt angle) |
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| 63 | o Optimize inplane rotations |
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| 64 | o Optimize all parameters |
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| 65 | o Mask region to only look at overlapping regions, overlap is shown on status bar |
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| 66 | o Hit Auto optimize, it performs find theta, optimize angles and mask in a single click |
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| 67 | o If you look at the Terminal it will tell you how many optimization rounds were performed |
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| 68 | o Use transfer picks button, this works but is based on the alignment parameters |
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| 69 | |||
| 70 | * Auto pick particles |
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| 71 | o Measure particle size using ruler tool, zoom in to get best value |
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| 72 | o Run DoG picker with wrong contrast |
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| 73 | o Reject picks |
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| 74 | o Run DoG picker with correct contrast |
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| 75 | o Show terminal |
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| 76 | o Accept picks |
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| 77 | o Look at DoG map images |
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| 78 | |||
| 79 | * Clean up particle picks |
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| 80 | o Use clear bad picks button |
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| 81 | o Use polygon tool |
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| 82 | o Auto optimize |
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| 83 | o Use cutoff button to remove picks below a threshold |
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| 84 | o Add more picks |
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| 85 | o Save and quit |