Tomogram Subvolume Alignment and Averaging with PEET

University of Colorado, Boulder


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

Description of PEET

PEET (Particle Estimation for Electron Tomography) is an open-source package for aligning and averaging particles in 3-D volumes extracted from tomograms. It seeks the optimal alignment of each particle against 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. PEET 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 more 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 Group

The PEET discussion group provides a forum for registered users to ask and answer questions, to share their experiences, and to receive notification of new releases and other PEET news. Digests and posting via email (i.e. list server functionality) are provided. Additional capabilities, including browsable / searchable archives are available through a web interface. Access to the web interface requires a Google login profile, which must be associated with the email address at which you wish to be contacted. (Non Gmail addresses can be used with a Google login, with or without a Gmail address. See the Email section of your Google Account settings). The group is not moderated, but joining requires approval.

To subscribe or visit the group via the web interface please visit PEET-LIST. If you do not have and are not willing to create a Google login and are satisfied with email only access, you can also request membership by sending an email to peet-list+subscribe@g.colorado.edu. Supplemental confirmation of your identity may be required for email subscriptions.

After your request is approved, you will be added to the group and will receive a confirmation email with additional instructions. Once subscribed, we request that you edit your membership settings for this group so that your display name is your real name. To post to the forum you can either use the web interface or simply email your posting to peet-list@colorado.edu

To cancel your subscription, use the web interface or send an email to peet-list+unsubscribe@g.colorado.edu.

When replying to a previous posting via email, you will have the option to reply to the sender or to the list. Private replies may be appropriate for preliminary discussions, but please sure to post any final solutions or workarounds to the group so they will be available to everyone.

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 http://bio3d.colorado.edu/ftp/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 set of introductory tutorials can be downloaded from http://bio3d.colorado.edu/ftp/PEET/tutorials/ or viewed on our YouTube channel at http://www.youtube.com/BL3DEMC. The associated sample data sets can be downloaded from http://bio3d.colorado.edu/ftp/PEET/sampleDatasets/.

Submitting a Bug or Requesting Help

Defect submissions and requests for help are always welcome. While the PEET Discussion Group is the main venue for support, requests can also be emailed directly to to john.heumann@colorado.edu. We reserve the right to forward direct requests (after anonymization, if requested) to the discussion group if we feel they are of broader interest.

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. 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.

Ideally, attach or upload to the discussion group a tomosnapshot (from eTomo, press 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 much more likely to contain the necessary information.