Supported Applications
SPHIRE
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Description
(SParx for HIgh Resolution Electron microscopy) a tool 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
To list all executables provided by SPHIRE, run:$ sbgrid-list sphire
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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
Due to BDB depreciation, EMAN2 2.91 or 2.07 should be used with SPHIRE.
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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 (1.2 KB) -
Other Versions
Linux 64:
1.3 (1.3 KB) -
OS X INTEL:
1.3 (1.2 KB)
Developers
Christos Gatsogiannis, Felipe Merino, Markus Stabrin, Michael Saur, Pawel Penczek, Stefan Raunser, Toshio Moriya, Zhong Huang