HHMI UCB LBL

Adapt

This gzipped tar archive contains the source required to compile an image classification program based on the work of Ogura et al (see references). It is written in C++ and includes a README file that covers its operation.

The program can also be used in the generation of classes for Random Conical Tilt or Orthogonal Tilt Reconstruction using SPIDER.

Adapt is a piece of working, in-house software and as such hasn't been extensively tested on many hardware setups and systems.

Note: Release 2.02 compiles cleanly under gcc 4.3.x and includes a bugfix for a segfault condition in the previous releasee.


Usage

Required Inputs

  • an IMAGIC image stack, most likely the output of a multi-re2ference alignment (MRA), to be classified into groups.
  • various parameters of classification described in the README and Ogura paper.
  • the number of nodes in the network (e.g., the number of classes wanted).

Outputs

  • an IMAGIC image stack corresponding to 'node images' (see Ogura paper)
  • an IMAGIC image stack of class averages
  • SPIDER format select files for each class.

References

Ramey VH, Wang HW, Nogales E. (2009) Ab initio reconstruction of helical samples with heterogeneity, disorder and coexisting symmetries. J Struct Biol., E-pub ahead of print.

Ogura T, Iwasaki K, Sato C. (2003) Topology representing network enables highly accurate classification of protein images taken by cryo electron-microscope without masking. J Struct Biol., 143(3), 185-200.


Download

Download Adapt2_02_mp.tar.gz (12k)
View README


News

Recent publications

Kellogg et al. <a href=http://www.sciencedirect.com/science/article/pii/S0022283617300153\> Insights into the Distinct Mechanisms of Action of Taxane and Non-Taxane Microtubule Stabilizers from Cryo-EM Structures</a><i> JCB</i>, 2017 Mar 10; Epub ahead of print Yuan et al. <a href=http://www.nature.com/nature/journal/v533/n7603/full/nature17970.html\> Near-atomic resolution visualization of human transcription promoter opening</a><i> Nature</i>, 2016 May 11; Epub ahead of print Louder et al. <a href=http://www.ncbi.nlm.nih.gov/pubmed/27007846> Structure of promoter-bound TFIID and model of human pre-initiation complex assembly</a><i> Nature</i>, 2016 Mar 23;531(7596):604-9 Jiang and Taylor et al. <a href=http://www.ncbi.nlm.nih.gov/pubmed/26841432> Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage.</a> <i>Science</i>, Jan 2016; Epub ahead of print Nogales and Zhang<a href=http://www.sciencedirect.com/science/article/pii/S0959440X16000038> Visualizing microtubule structural transitions and interactions with associated proteins</a> <i>COSB</i>, April 2016; <b>37</b>, 90-96  Zhang et al. <a href=http://www.sciencedirect.com/science/article/pii/S0092867415008491> Mechanistic origin of microtubule dynamic instability and its modulation by EB proteins</a><i> Cell 2015 Aug 13;162(4):849-59

Eva Nogales has been elected to the American Academy of Arts and Sciences

Basil Greber and Kelly Nguyen have won the 2016 RNA Society Scaringe Award

Eva Nogales has won the 2016 Mildred Cohn Award in biological chemistry from the American Society for Biochemistry and Molecular Biology

Harvey Lecture by Eva Nogales