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| [[#args|Command line arguments]] |  [[#checkfunc|Check functionality]] | [[EMAN2:e2simmx2stagefaq|e2simmx2stage FAQ]] |

===== e2simmx2stage =====
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This program computes a similarity matrix similar to e2simmx, but in this case, the matrix is sparse to make the computation faster. The populated regions will correspond to the best similarity values.

<<Anchor(args)>>

==== Command Line Arguments ====
e2simmx2stage.py [options] <c input> <r input> <output> <ref simmx> <stg1 refs> <stg1 simmx>

For command line options, see [[EMAN2:Programs/e2simmx|e2simmx.py]]

<c input> <r input> <output> are the same as in e2simmx.py <ref simmx> - Similarity between the various reference images used to generate the stage 1 references and classification tree <stg1 refs> - References used for the coarse stage 1 similarity search <stg1 simmx> - Similarity matrix for all particles vs the stage 1 references

Anticipated speedups for this prorgram vs. e2simmx.py when no stage1 shrinking is used:

{{http://blake.bcm.edu/dl/EMAN2/speedup.jpg}}