Xmipp

List of all Xmipp programs v3.0

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

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.