Filament Particle-Picker

Introduction

[Inspirational text will appear here]

Screenshot

Caption: tracing helical segments of the Agrobacterium Tumefaciens T-Complex.

Requirements

This software will run anywhere that MATLAB is available. You will need the `mex compiler' to compile spi_read (to read SPIDER files into Matlab), although you can download binaries for x86 linux from the spi_file web page.

Distribution

If you find this software useful or interesting, I would appreciate it if you could send me a short email. My general address is tobin@splorg.org.

main.m — the graphical tool for filament selection
You'll also need my spi_file library to read SPIDER files into Matlab
pick_from_state.m — process a 'state' object, running the `filament_follow' particle-picker on each filament
filament_follow.m — simple picker to output regularly spaced `particles' along a filament
state_display.m — very simple program to output the contents of a `state' object (a tree of files, each containing filaments, which contain verticies)

Instructions

[nonexistant at this point]

The entire state of your selections within the Filament Picker is stored in a variable called `state', a complex object (`struct') that keeps track of the files you have loaded, the filaments (`groups') you have defined for each file, and the verticies of each filament. When you use the 'Save' button in the Filament Picker, the state object is written to a Matlab (.mat) file of your choice. In the following example the filename is "state.mat".

>> load('state.mat')
>> who

Your variables are:

ans    state  

>> state

state = 

          files: [1x2 struct]
    currentfile: 2
      lastgroup: 5

>> state_display(state)
 +----File /home/tobin/projects/guitool/data/uacH8sptl_001.spi
 |     Group 1 (6 verticies)
 |     Group 2 (17 verticies)
 |     Group 3 (3 verticies)
 |     Group 4 (5 verticies)
 +----File /home/tobin/projects/guitool/data/uacH8sptl_002.spi
 |     Group 5 (0 verticies)

Acknowledgements

This program was developed during summer 2002 while I was student at the Karyn Kupcinet International Science School at the Weizmann Institute of Science in Rehovot, Israel.