Segment Volume

Introduction

The Segment Volume package is a tool designed for segmenting 3D volume data. The package consists of modules which are Chimera extension modules. To use these modules, you will need the Chimera and EMAN software packages to use this module.

Note: This is pre-release version of the Segment Volume package.

Package contents

• Segment Simple module
• Segment Marker module
• Segment Read module
• Segment Write module
• Track Transform module
• Segment Mask module
• Dock Manual module
• Measure Stick module

Startup

Listing the module

To list the module under Chimera's Tools menu, add the directory - containing - the modules directories (eg: Segment Simple module is in the directory SegmentSimple) directory to Chimera's list of Tools.

To do so, open Chimera's main window, choose Perferences under Favorites menu, then choose the Tools category and then Add the directory - containing - the module directories. This will list the tools under AIRS on the Tools menu.

Starting the module

To start a module from the Chimera menu, first you will need to ensure that the module is listed under Chimera's Tools menu. Then, click on the module name in the AIRS menu, under Chimera's Tools menu.

Debugging

To debug the package, you can run a small script file that will produce a text message. Please follow the instructions in the message or email the text message along with any error messages.

To run the debug file, locate the file named debug.py in the SegmentDebug sub-directory of Airs-Segment directory in the chimera extension for EMAN.

Then run the script file by first launching the IDLE program in Chimera. From the Chimera Tools menu, locate IDLE under one of the menu items, and click on it.

Now, from the command line, type execfile([FULL PATH TO DEBUG SCRIPT FILE]).

For example, if the path is /home/user/EMAN/chimeraext/Airs-Segment/SegmentDebug/debug.py, then type: execfile('/home/user/EMAN/chimeraext/Airs-Segment/SegmentDebug/debug.py')