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eman2:eman1transition_eman1v2 [2025/07/04 20:07] – created steveludtkeeman2:eman1transition_eman1v2 [2025/07/04 20:14] (current) – steveludtke
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 +**//WARNING: This page was written in the early days of EMAN2 and some of its concepts are no longer accurate. For example, the BDB database system was retired over a decade ago in favor of HDF and LST files. There are still some useful things here, but take them with a grain of salt.//**
 +
 ====== An overview of changes between EMAN1 and EMAN2 ====== ====== An overview of changes between EMAN1 and EMAN2 ======
  
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   * All EMAN2 command-line programs, including the GUI, are written in Python, which gives advanced users a lot of flexibility without having to recompile EMAN2 from source.   * All EMAN2 command-line programs, including the GUI, are written in Python, which gives advanced users a lot of flexibility without having to recompile EMAN2 from source.
   * The command-line options in EMAN2 have adopted the standard Unix style rather than the EMAN1 style, for example 'proc2d abc.hed def.spi clip=64,64' has become 'e2proc2d.py abc.hed def.spi --clip=64,64'. In many, but not all, cases, the option names are the same.   * The command-line options in EMAN2 have adopted the standard Unix style rather than the EMAN1 style, for example 'proc2d abc.hed def.spi clip=64,64' has become 'e2proc2d.py abc.hed def.spi --clip=64,64'. In many, but not all, cases, the option names are the same.
-  * While EMAN2 supports all of the [[Eman2DataStorage|file formats]] (and more) from EMAN1, if you wish to make sure all of the metadata is stored during processing, you must use either HDF or the BDB database. +  * While EMAN2 supports all of the [[Eman2DataStorage|file formats]] (and more) from EMAN1, if you wish to make sure all of the metadata is stored during processing, you must use either HDF or the BDB database. 
-  * EMAN2 uses an [[EMAN2:DatabaseWarning|embedded (no database server) database system]] for storing a lot of image data and metadata. This system is  extremely useful and powerful, but at times can also be very frustrating and irritating. +
   * EMAN2 supports a modular system for parallel processing, and can support:   * EMAN2 supports a modular system for parallel processing, and can support:
     * multi-cpu (threaded) parallelism on the local computer     * multi-cpu (threaded) parallelism on the local computer
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 frustrating. In EMAN2, we try to preserve everything computed during the refinement (with a few impractical exceptions). frustrating. In EMAN2, we try to preserve everything computed during the refinement (with a few impractical exceptions).
 While this can take a lot of extra disk space during processing, you are always free to delete any intermediate files you While this can take a lot of extra disk space during processing, you are always free to delete any intermediate files you
-don't want and increasingly, disk space is cheap. The [[EMAN2|EMAN2 Wiki]] contains pages documenting everything we store:+don't want and increasingly, disk space is cheap. The [[eman2:|EMAN2 Wiki]] contains pages documenting everything we store:
   * [[Eman2Metadata|metadata stored in image headers]]   * [[Eman2Metadata|metadata stored in image headers]]
-  * [[Eman2AppMetadata|metadata associated with a project]]+  * [[AppMetadata|metadata associated with a project]]
   * [[EMAN2:Concepts|information on intermediate files, conventions, etc.]]   * [[EMAN2:Concepts|information on intermediate files, conventions, etc.]]
  
eman2/eman1transition_eman1v2.1751659674.txt.gz · Last modified: by steveludtke