Supported Applications
SPHIRE
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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).
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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
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Installation
Use the following command to install this title with the CLI client:$ sbgrid-cli install sphire
Available operating systems: Linux 64, OS X INTEL -
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.
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*Full citation information available through
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Tales
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Webinars
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Keywords
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Default Versions
Linux 64:  1.4 (1.3 KB)
OS X INTEL:  1.4 (1.1 KB) -
Other Versions
Linux 64:
1.3 (1.3 KB) -
OS X INTEL:
1.3 (1.1 KB)
Developers
Christos Gatsogiannis, Felipe Merino, Markus Stabrin, Michael Saur, Pawel Penczek, Stefan Raunser, Toshio Moriya, Zhong Huang