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EMAN Reconstruction - Phase 3


In this step we seek to refine our preliminary model to generate a final, (hopefully) high resolution, structure.

1. Run the 'refine' command.

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At this point you only need 2 files your working directory. If you'd like you can remove the others, but it's not really necessary. start.hed/img contains the raw particle data (preprocessed with ctfit), and threed.0a.mrc contains the preliminary 3d model you generated in the last step. The refine command is fairly complecated and has a lot of options. For now, we'll start with a basic refine command which should work well in most cases. Generally it's a good idea to run this command from a screen window, or submit it as a background job with nohup and '&' (see man page). You can monitor the progress of the run with eman, by looking at the command history. refine will run numerous other eman programs, much like a script, while it executes. Each of these individual programs will appear in the program history. The end of one refinement iteration is marked by the completion of a proc3d command.

Here's the refine command to run for your particle: $1n

At this point you only need 2 files your working directory. If you'd like you can remove the others, but it's not really necessary. start.hed/img contains the raw particle data (filtered earlier), and threed.0a.mrc contains the preliminary 3d model you generated in the last step. The refine command is fairly complecated and has a lot of options. For now, we'll start with a basic refine command which should work well in most cases. Generally it's a good idea to run this command from a screen window, or submit it as a background job with nohup and '&' (see man page). You can monitor the progress of the run with eman, by looking at the command history. refine will run numerous other eman programs, much like a script, while it executes. Each of these individual programs will appear in the program history. The end of one refinement iteration is marked by the completion of a proc3d command.

Here's the refine command to run for your particle: $2

If you have a good feel for the size of your particle, you can replace the '-1' in mask=-1 with a safe mask radius for your macromolecule.

Look at the refine documentation for info on all of the parameters, but there are a few basics you should be aware of:

There are also a number of new refine options in this version of EMAN. These options are still considered experimental, but in some cases one or more may make a dramatic improvement in refinement quality.

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