Scripts for Bsoft programs

Intensive data processing tasks that require large amounts of time and memory can be distributed in various ways. These scripts provide ways to process data in pieces or subsets, either on one computer or through a distributed processing system.

To retrieve a script, open it in a web page and copy the text to a text editor. Save the text file without an extension (e.g., "bomrun" or "tomrec"). Make the script executable:

chmod u+x bomrun

Place the script in an accessible directory (such as ~/bin or /usr/local/bin).

Single particle analysis

The processing for single particle reconstructions in Bsoft can be automated as three phases:

Phase 1: Preprocessing

The particular operations required for preprocessing depends on the way micrographs were taken. The details in the following scripts therefore need to be modified.

The script mgpick provides for optional gain correction, binning, frame alignment, power spectrum calculation and CTF fitting of a set of micrographs. To distribute it over a system such as Peach, use a driver script, e.g., pdrvr:

pdrvr *.mrc

Phase 2: Particle picking

Similar to preprocessing, a script, mgpick, can be used with a driver script to distribute the particle picking across a distributed processing system.

Phase 3: Alignment and reconstruction

This phase is usually run as iterated units of alignment, particle selection, reconstruction and resolution assessment. At the moment automation has not been fully worked out and the best is to run each iteration separately. The following are scripts used to distribute alignment with borient and brefine across Peach:

  1. borient: bomrun
  2. brefine: brefrun