Tomogram Subvolume Alignment and Averaging with PEET

Boulder Laboratory for 3-D Electron Microscopy of Cells


Description of PEET
Publications
PEET Discussion List
Documentation for PEET
Submitting a Bug or Requesting Help
Download

Description of PEET

PEET (Particle Estimation for Electron Tomography) is a package for aligning and averaging particles in 3-D volumes extracted from tomograms. It finds the optimal alignment of each particle with a reference volume through several iterations. If PEET and IMOD are both installed, most PEET operations are available from the eTomo graphical user interface in IMOD. PEET uses the parallel processing framework within IMOD, so that the lengthy computations can be distributed to multiple cores on one computer, to a set of linked workstations, or to a cluster. It is written in Matlab and a compiled version is distributed along with the Matlab runtime environment needed to run it.

Publications

PEET was first applied for averaging axonemes and its methods were described in:

Nicastro, D., C. Schwartz, J. Pierson, R. Gaudette, M.E. Porter and J.R. McIntosh (2006) The molecular architecture of axonemes revealed by cryoelectron tomography. Science. 313: 944-948.

Please cite this paper if you use PEET in your research. The package has developed considerably since, with applications to isolated particles as well as ones along fibers. Some recent applications are described in:

Xiong, Q., M. K. Morphew, C. L. Schwartz, A. H. Hoenger, D. N. Mastronarde (2009) CTF determination and correction for low dose tomographic tilt series. J. Struct. Biol. 168: 378-87.

Cope, J., S. Gilbert, I. Rayment, D. Mastronarde, A. Hoenger (2010) Cryo-electron tomography of microtubule-kinesin motor complexes. J. Struct. Biol. 170: 257-65.

PEET Discussion List

The PEET discussion listserver provides a means for users to ask questions and share their experiences, as well as a way to receive notification of new releases and other news. The list is not moderated, but joining requires approval.

To subscribe to this list, send a message to listproc@lists.Colorado.EDU with the contents of your message being:

subscribe peet-list your-full-name

where your-full-name is your first name followed by your last name, including any punctuation and spaces. After your request is approved, you will be added to the list and will receive an email with more instructions on using the list.

To post to the list, send an email (plain text, not html) addressed to peet-list@lists.colorado.edu.

To remove yourself from the list, send a message to listproc@lists.Colorado.EDU with the contents of the message being:

unsubscribe peet-list

To access the list archives, see these instructions.

Documentation for PEET

Man pages are available in both ASCII and html formats for each of the programs comprising PEET. These pages ship with PEET, and can also be viewed online here, or downloaded from the "man" subdirectory of ftp://bio3d.colorado.edu/pub/PEET/ A guide for running PEET through the eTomo graphical user interface can be found here. This guide is distributed in IMOD and can be opened from the Help menu in eTomo once PEET has been installed. A growing set of introductory tutorials can be downloaded from ftp://bio3d.colorado.edu/pub/PEET/tutorials/ or viewed on our YouTube channel at http://www.youtube.com/BL3DEMC. The associated sample data sets can be downloaded from ftp://bio3d.colorado.edu/pub/PEET/sampleDatasets/.

Submitting a Bug or Requesting Help

Defect submissions and requests for help are always welcome. They can be sent to the discussion list or emailed to heumannj@colorado.edu or mast@colorado.edu. We try to provide excellent responsiveness and customer service. You can help considerably by making sure your requests are clear and complete. Before submitting, please consider the following. 1) Have you updated to the most recent supported versions of PEET and IMOD and verified that the problem still exists there? If not, please do so before submitting. Considerable time and effort are wasted repeatedly tracking down bugs which already been fixed. 2) Please be as explicit as possible. Describe exactly what you were doing, what the problem you encountered was, and, if possible, how to reproduce it. At a minimum, always include a description of the hardware you are running on, the operating system name and version, and both PEET and IMOD versions. When emailing heumannj@colorado.edu or mast@colorado.edu, please include an tomosnapshot (File / Run Tomosnapshot) taken in the PEET project directory immediately after the error occured. Screen shots can be included if desired, but are rarely helpful; a tomosnapshot is more likely to contain the necessary information.