Content-type: text/html Manpage of createAlignedModel


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createAlignedModel - generate model(s) and motive list(s) containing the results of a previous alignment.  


createAlignedModel filename
createAlignedModel filename iterationNumber
createAlignedModel filename iterationNumber minCCC  


CreateAlignedModel will generate new model and motive list file(s) containing locations and orientations found at alignment iteration 'iterationNumber' using settings specified in parameter file 'filename'. Cross-correlation scores for each particle will be inserted as values for each point in the new model, so they can be displayed in pseudo-color using 3dmod. Updated versions of rotation axes files present in the project directory will also be created, reflecting the new alignment and particle selection.

The new model and motive list for the tomogram 'N' and iteration number 'M' will be named




respectively, where <fnModParticle(N)> refers to the model specified for the Nth volume in the parameter file. Additionally, a summary csv file containing the contour number, particle coordinates, and Z-Y-X Slicer angles (in the order X, Y, Z) required to rotate the reference to the orientation of the particle will written to


This summary file is useful as input to IMOD programs clonemodel and clonevolume. (Both the input model name and the tomogram number are included in output names, since multiple tomograms can refer to the same input model).

A rotation axes file <fnOutput>_Tom<N>_RotAxes.csv will be udpated and the new version stored in <fnOutput>_Tom<N>_Iter<iterNum>_RotAxes.csv. Only rotation files located in the project directory and following this naming convention will be automatically updated.

The file name of the parameter file. See PEET man page and below for descriptions of applicable parameter file settings.
iterationNumber (optional)
An integer specifying the alignment iteration whose output will determine the rotations and translations used to compute the reference and/or average volumes. If omitted, the output of the final search iteration specified in
 the parameter file will be used.
minCCC (optional)
The minimum cross-correlation score a particle must have for inclusion in the alignment model.

CreateAlignedModel supports the debugLevel, fnModParticle, fnOutput, flgRemoveDuplicates, and flgVolNamesAreTemplates parameter file settings, described in the PEET man page, plus the following additional setting:

selectClassID = integer vector
The class ID(s) of particles to be included in the output. If not empty, all other particle classes will be excluded. By default, any particles flagged as duplicates (see the man page for removeDuplicates), will be ignored unless the duplicate class ID (-9999) is included in selectClassID.


John Heumann  


PEET(1), prepareEM(1), prepareRef(1), mergeEM(1), alignSubset(1), removeDuplicates(1), calcFSC(1), and calcSSNR(1)




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Time: 21:10:05 GMT, March 20, 2017