Project

General

Profile

TiltPicker Usage » History » Version 4

Neil Voss, 04/15/2010 08:28 AM

1 3 Neil Voss
======================
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:
6 1 Neil Voss
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
12
13
If all works the picker will open up and you'll have two images of ribosomes.
14
15
======================
16 4 Neil Voss
h2. BUG TRACKING:
17 3 Neil Voss
======================
18
19
 TiltPicker bugs are now tracked via the AMI redmine server, visit
20
 http://emg.nysbc.org/projects/tiltpicker/
21
 to file any bugs
22
23
======================
24 4 Neil Voss
h2. YOUTUBE MOVIE:
25 3 Neil Voss
======================
26
27
I just made a screen capture video on how to use it. It is available is low resolution on youtube:
28
29
 http://www.youtube.com/watch?v=cw1osPBY_JM
30
31
or you can download the full screen version from the appion.org website:
32
33
 http://code.google.com/p/appion/downloads/list
34
35
I recommend using VLC to watch it:
36
37
 http://www.videolan.org/vlc/
38
39
======================
40 4 Neil Voss
h2. STEP BY STEP TUTORIAL:
41 3 Neil Voss
======================
42
43
TiltPicker Usage
44
45
    * Start TiltPicker
46
          o Extract TiltPicker, on command line type:
47
            tar -zxf tiltpicker-2.0.tgz
48
          o Go to tiltpicker directory, on command line type:
49
            cd tiltpicker
50
          o Display TiltPicker help, on command line type:
51
            ./ApTiltPicker.py -h
52
          o Open TiltPicker, on command line type:
53
            ./ApTiltPicker.py -l data/rawu048b.jpg -r data/rawu049b.jpg -t 50.0
54
55
    * Initialize alignment:
56
          o Maximize window
57
          o Set correct zoom for images
58
          o Center the middle bar
59
          o Pick 5 partcle pairs
60
          o Save picks to a file
61
          o Hit the apply button, circles will not match crosses
62
          o Find theta (tilt angle)
63
          o Optimize inplane rotations
64
          o Optimize all parameters
65
          o Mask region to only look at overlapping regions, overlap is shown on status bar
66
          o Hit Auto optimize, it performs find theta, optimize angles and mask in a single click
67
          o If you look at the Terminal it will tell you how many optimization rounds were performed
68
          o Use transfer picks button, this works but is based on the alignment parameters
69
70
    * Auto pick particles
71
          o Measure particle size using ruler tool, zoom in to get best value
72
          o Run DoG picker with wrong contrast
73
          o Reject picks
74
          o Run DoG picker with correct contrast
75
          o Show terminal
76
          o Accept picks
77
          o Look at DoG map images
78
79
    * Clean up particle picks
80
          o Use clear bad picks button
81
          o Use polygon tool
82
          o Auto optimize
83
          o Use cutoff button to remove picks below a threshold
84
          o Add more picks
85
          o Save and quit