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| This page describes some important concepts in EMAN2 | * [[EMAN2/ProjectDatabase|Projects, e2desktop.py and the database]] * [[EMAN2/BoxSize|Particle box-size and refinement speed, what size to use]] * [[EMAN2/Symmetry|EMAN2 and the asymmetric unit]] * [[Eman2DataStorage|File Formats, Data storage conventions, and the internal database (what is BDB: ?)]] * [[Eman2NFS|Practical Advice on EMAN2 in environments with network-shared directories (like NFS)]] * [[EMAN2/CtfModel|CTF model used in EMAN2]] * [[Eman2TransformInPython|Transformations in the context of projections, reconstructions, and in general]] * [[EMAN2/AlignersDescription|More information regarding the aligners]] * [[Eman2Metadata|Parameters/Metadata appearing in EMData attributes (and stored on disk with the image), accessed with get_attr and set_attr]] * [[Eman2AppMetadata|Parameters/Metadata for applications, not associated with a specific image, stored in bdb:project]] |
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| * [:EMAN2/Symmetry:EMAN2 and the asymmetric unit] * [:EMAN2/TransformConventions:Transformations in the context of projections, reconstructions, and in general] * [:EMAN2/AlignersDescription:More information regarding the aligners] |
=== Information on specific files used in 3-D single particle refinement === This section documents the contents of all of the files produced by running e2refine.py in one of the refine_xx directories. * [[EMAN2/ProjectionFiles|Map projection files (projections_xx, proj_stg1_xx)]] * [[EMAN2/SimmxFiles|Similarity matrix image files (simmx_xx, simmx_stg1_xx, proj_simmx_xx)]] * [[EMAN2/ClassmxFiles|Classification matrix image files (classify_xx)]] * [[EMAN2/ClsResultFiles|Class-Averaging Results matrix image files (cls_result_xx)]] * [[EMAN2/ClassesFiles|Class-averages (classes_xx)]] * [[EMAN2/ThreedFiles|3-D reconstructions (threed_xx, threed_filt_xx, threed_mask_xx)]] {{attachment:single_image_iso_c.png}} |
EMAN2 Concepts and Conventions
File Formats, Data storage conventions, and the internal database (what is BDB: ?)
Practical Advice on EMAN2 in environments with network-shared directories (like NFS)
Transformations in the context of projections, reconstructions, and in general
Parameters/Metadata for applications, not associated with a specific image, stored in bdb:project
Information on specific files used in 3-D single particle refinement
This section documents the contents of all of the files produced by running e2refine.py in one of the refine_xx directories.
Similarity matrix image files (simmx_xx, simmx_stg1_xx, proj_simmx_xx)
3-D reconstructions (threed_xx, threed_filt_xx, threed_mask_xx)
