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

Liu JJ et al. <a href=https://www.nature.com/articles/s41586-019-0908-x> CasX enzymes comprise a distinct family of RNA-guided genome editors </a> Nature 2019 Feb 04 Patel et al. <a href=http://science.sciencemag.org/content/early/2018/11/14/science.aau8872> Structure of human TFIID and mechanism of TBP loading onto promoter DNA </a> Science 2018 Nov 15 Kellogg et al. <a href=http://science.sciencemag.org/content/early/2018/05/09/science.aat1780?rss=1> Near-atomic model of microtubule-tau interactions </a> Science 2018 May 10 Nguyen et al. <a href= https://www.nature.com/articles/s41586-018-0062-x>  Cryo-EM structure of substrate-bound human telomerase holoenzyme.
</a> Nature 2018 Apr 25 Poepsel et al. <a href=https://www.nature.com/articles/s41594-018-0023-y > Cryo-EM structures of PRC2 simultaneously engaged with two functionally distinct nucleosomes. </a> Nature Structural and Molecular Biology 2018 Jan 29 Kasinath et al. <a href=http://science.sciencemag.org/content/early/2018/01/17/science.aar5700 > Structures of human PRC2 with its cofactors AEBP2 and JARID2. </a> Science 2018 Jan 18

Lab member, Basil Greber , will be an ICR Fellow, in the Division of Structural Biology at the Institute of Cancer Research, London, UK

Lab Memeber, Vignesh Kasinath , will be starting as an Assistant Professor in the Department of Biochemistry at CU Boulder

Eva Nogales Named a 2020 Biophysical Society Fellow EMBO

Lab Member, Vignesh Kasinath has been awarded the the NIH Pathway to Independence (K99) award

Lab Member, Kelly Nguyen , will be starting as a Group Leader at the MRC-Laboratory of Molecular Biology in Cambridge, UK in August 2019

Lab member, Simon Poepsel, has started an Independent Research Group at the Center for Molecular Medicine at the University of Cologne, Germany in June 2019