SubTomogramAverageMPI

SubTomogramAverageMPI is a command line program used for subtomogram alignment and averaging. Alignment sources, output destinations and parameters are defined in a Artiatomi-style config-file, which is provided to the program as a command line argument.

Table of Contents Installation System Requirements Algorithm Parameters Input to the Program General Requirements Command Line Input Config-File Input Output from the Program Usage Example Comments

Installation

System Requirements

• nVidia CUDA 8.0 toolkit
• Multiple GPUs with a total memory size of the volume to reconstruct (16 or 32 bits per voxel) + some memory for the projection images. (We use four GeForce Titan X with 12 GByte each).
• Enough RAM on host: There is no hard limit, but the more memory is available, the bigger the reconstruction can be.
• OpenMPI 1.10.2 installed for multi-GPU support.

Algorithm

Parameters

Input to the Program

General Requirements

File	Format	Information	Output from
Subtomograms	.em	Subtomograms to be aligned (density is dark)	Matlab function artia.particle.extract_write
Motivelist	.em	Particle list file	Particle picking pipeline.
Reference	.em	Initial reference to align subtomograms to.	AddParticles or manual generation.
Wedge-Filter	.em	Fourier space filter to use for missing wedge correction	Matlab functions artia.wedge.primitive and artia.wedge.dose_weighted
Mask	.em	Mask to be applied to particles	Matlab functions in artia.mask
MaskCC	.em	Filter to be applied to raw CC-maps to limit translational freedom	Matlab functions in artia.mask
config-file	.cfg	file to set all parameters that are used by the program	manual generation or matlab function artia.cfg.write

Command Line Input

-n MPIs	Set a number for MPIs. This describes how many MPI-processes are spawned by the program. The number has to be related to the number of CUDA devices specified in the config-file.
-u config-file.	Give the path to the config-file. The config-file contains all further parameters that are necessary for the execution of the program.

Config-File Input

Detailed descriptions for all parameters in the config-file can be found on the respective page.

Output from the Program

Usage

Example

Comments

Category:Software