Xmipp

List of all Xmipp programs v3.1

By Topic

Global parameters

  • Common options Options that are common to all Xmipp's programs
  • Common files Description of most commonly used files by Xmipp's programs

Interface

  • apropos Search the programs help and descriptions
  • browser Browse files in a directory
  • mpi_run Run commands in a parallel environment
  • projections_explorerj Visualize the projections as an angular distribution
  • protocols Create an Xmipp project
  • showj Display images, volumes, stacks, metadatas...etc, using ImageJ as graphical platform

Classification

CTF

Images

Metadatas

Phantoms and PDBs

Angular assignment

Tomography

Transformations

Volumes

Tools

  • compile Compile a C++ program using Xmipp libraries
  • sqlite3 Open a SQlite database

MPI

Several programs that are memory and cpu intensive have a parallel version based on MPI. Usually mpi_ is prefixed to the serial program's name. For example, if you want to run an MPI program in 10 nodes:

mpirun -np 10 xmipp_mpi_program <program_options>

Some MPI programs have an extra param --mpi_job_size that controls how the work is distributed between the different CPUs. Set it to a small number for large images and to a relatively high number for small images.

You can use the --help option for more details on each specific MPI program.