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eman2:programs_e2refine [2025/07/06 15:56] – steveludtkeeman2:programs_e2refine [2025/07/06 16:17] (current) – steveludtke
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 || ||--simalign||string||The name of an [[EMAN2:Modular:Aligners|aligner]] to use prior to comparing the images|| || ||--simalign||string||The name of an [[EMAN2:Modular:Aligners|aligner]] to use prior to comparing the images||
 || ||--simaligncmp||string||Name and options for a [[EMAN2:Modular:Cmps|comparator]] to use in first stage alignment for classification|| || ||--simaligncmp||string||Name and options for a [[EMAN2:Modular:Cmps|comparator]] to use in first stage alignment for classification||
-|| ||--simralign||string||The name and parameters of the second stage [[EMAN2:Modular/Aligners|aligner]] which refines the results of the first alignment. Currently this is either not specified or is 'refine'.||+|| ||--simralign||string||The name and parameters of the second stage [[EMAN2:Modular:Aligners|aligner]] which refines the results of the first alignment. Currently this is either not specified or is 'refine'.||
 || ||--simraligncmp||string||The name and parameters of the [[EMAN2:Modular:Cmps|comparator]] used by the second stage aligner. Default is dot.|| || ||--simraligncmp||string||The name and parameters of the [[EMAN2:Modular:Cmps|comparator]] used by the second stage aligner. Default is dot.||
 || ||--simmask||string||A file containing a single 0/1 image to apply as a mask before comparison but after alignment|| || ||--simmask||string||A file containing a single 0/1 image to apply as a mask before comparison but after alignment||
eman2/programs_e2refine.txt · Last modified: by steveludtke