Job: Align 3D maps

Align two or more 3D maps.


Use this tool to align two or more 3D maps to a common reference in order to better analyze maps obtained from different experiments. The maps do not need to come from the same type of job. For example, one could align a coarse resolution map obtained from ab-initio reconstruction with a higher resolution map obtained from refinement.


  • Reference Map

  • Map(s) to Align

  • (Optionally) Particles


  • Reference Map

  • Aligned Map(s)

  • (Optionally) Particles with updated alignments3D

Common Parameters

  • Update particle alignments will enable the option to update particle alignments3D values based on the computed 3D rigid body transform of each alignment. If this is turned on, additional particle inputs will be generated for all maps to be aligned.

  • Mask threshold factor should be set to a value between 0 and 1. This value will be used to create a mask around the density to exclude solvent during alignment.

  • Log rotation matrices, figures and difference maps will produce verbose output for the job.

Common Next Steps

  • Local Refinement

  • Homogeneous Reconstruction Only (to check that particle alignments are correct)

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