Differences

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--- eman2:programs_e2refine [2025/07/06 11:49] – steveludtke
+++ eman2:programs_e2refine [2025/07/06 16:17] (current) – steveludtke
@@ Line 22: / Line 22: @@
 || ||--mass||float||The mass of the particle in kilodaltons, used to run normalize.bymass. If unspecified nothing happens. Requires the --apix argument.||
 || ||--apix||float||The angstrom per pixel of the input particles. This argument is required if you specify the --mass argument. If unspecified, the convergence plot is generated using either the project apix, or an apix of 1.||
-|| ||--sym||string||[[EMAN2:Modular:Symmetry|Symmetry]] to be imposed throughout: c<n>, d<n>, h<n>, tet, oct, icos. Omit this option or specify 'c1' for asymmetric reconstructions. ||
+|| ||--sym||string||[[EMAN2:Symmetry|Symmetry]] to be imposed throughout: c<n>, d<n>, h<n>, tet, oct, icos. Omit this option or specify 'c1' for asymmetric reconstructions. ||
 || ||--lowmem||bool||Make limited use of memory when possible. Slight speed penalty.||
 ||-P||--parallel||string||Run in parallel, specify type:<option>=<value>:<option>:<value>. See [[EMAN2:Parallel]]||
 === Options related to making projections ===
-See also [[EMAN2:Programs/e2project3d]]
+See also [[EMAN2:Programs:e2project3d]]
 || ||--projector||string||[[EMAN2:Modular:Projectors|Projector]] to use. 'standard' is the default||
-|| ||--orientgen||string||The [[EMAN2:Modular/OrientGens|orientation generation]] argument for e2project3d.py. Typically something like: //--orientgen=eman:delta=2.0:inc_mirror=0//||
+|| ||--orientgen||string||The [[eman2:modular:orientgens|orientation generation]] argument for e2project3d.py. Typically something like: //--orientgen=eman:delta=2.0:inc_mirror=0//||
 These  parameters are used by e2project3d. Several orientation generation techniques provide alternative methods for distributing orientations in the asymmetric unit. Orientations can be generated based on your desired angular spacing, or alternatively on the desired total number of projections. In the latter case EMAN2 will generate a number as close as possible to the specified number, but note that there is no guarantee of a perfect match. You can also vary the method by which projections are generated. If you check the 'include mirror' option you should be sure to use aligners to that do not perform mirror alignment.
@@ Line 40: / Line 40: @@
 || ||--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||
-|| ||--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.||
 || ||--simmask||string||A file containing a single 0/1 image to apply as a mask before comparison but after alignment||