Supported Applications

Description

(SParx for HIgh Resolution Electron microscopy) for cryoEM using statistical resampling to attain quality assessment and result reproducibility. Includes movie frame alignments (movie), CTF estimation of raw electron micrographs (cter), picking/stack creation (window), reproducible 2-D classification (isac), reproducible initial model generation (viper), automatic gold-standard 3-D refinement (meridien), local resolution estimation and filtering (localres), and up to the 3-D sorting of different conformational states based on the statistical 3-D variability of the data (sort3D).

Usage

Usage Notes

Running GPU-accelerated ISAC2 (linux-only):

sxisac2_gpu.py requires use of mpirun from eman2 (mpirun.eman2) and explicit specification of the GPU IDs. For example: mpirun.eman2 -n 4 sp_isac2_gpu.py bdb:isac_dummy_data_64#faces dummy_test5 --radius=32 --img_per_grp=8 --gpu_devices=0,1 specifies 2 GPU cards with IDs 0 and 1.

This is example uses the data described in the ISAC tutorial found here: https://sphire.mpg.de/wiki/doku.php?id=gpu_isac

Due to BDB depreciation, EMAN2 2.91 or 2.07 should be used with SPHIRE.

Installation

Primary Citation*

T. Moriya, M. Saur, M. Stabrin, F. Merino, H. Voicu, Z. Huang, P. A. Penczek, S. Raunser, and C. Gatsogiannis. 2017. High-resolution Single Particle Analysis from Electron Cryo-microscopy Images Using SPHIRE. Journal of Visualized Experiments.

• 
  *Full citation information available through

• AppCiter

Tales

Particle catcher

If insects had horror movies, one of the scariest would feature tiny monsters. The grisly drama would spotlight the real-life threat to insects from young threadworms, smaller than eyelashes, and their symbiotic gut bacteria. The worms seek out and penetrate insect larvae. Inside the larvae, the worms release their gut bacteria, Photorhabdus luminescens, named for their mysterious glow. The bacteria take over, emitting a slew of toxic proteins that quickly kill the insect. The bacteria thrive on the insect cadaver. In turn, the worms feast on the multiplying bacteria, reproduce, and move on to the next larvae. The setting would be a farm, because the worm and its bacteria are deployed as biological pest controls. But one of the bacteria’s toxic complexes has potential for medical use in … Read the full story here.

Webinars

Topic: SPHIRE: User-friendly pipeline for near-atomic resolution Cryo-EM structure determination with automatic validation mechanisms.
Speaker: Toshio Moriya, Ph.D. Postdoctoral Fellow, Max Planck Institute of Molecular Physiology

Host: Jason Key
Recorded on: October 10, 2017