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| == e2refine == | == e2refine2d == |
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| || {{attachment:e2refine.png}} || | |
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| e2refine2d.py runs in much the same way as refine2d.py, though it has beein improved in a number of subtle ways in [[EMAN1]] | |
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| e2refine.py runs in much the same way as [[EMAN1/Programs/Refine|refine]] in [[EMAN1]] | This program will take a set of boxed out particle images and perform iterative reference-free classification to produce a set of representative class-averages. The point of this process is to reduce noise levels, so the overall shape of the particle views present in the data can be better observed. Generally cryo-EM single particles are noisy enough that it is difficult to distinguish subtle, or even not-so-subtle differences between particle images. By aligning and averaging similar particles together, less noisy versions of representative views are created. The class-averages produced by this program are typically used for: |
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| This programs oversees iterative single particle reconstruction. The overall process is to take a pre-existing 3D image and a set of 2D images and to run a variety of (often intensive) image processing applications which produces a refined 3D model. In particular, the program iteratively executes a sequence of python scripts which perform specific tasks, starting with with 3D projection (e2project3d.py), comparision of particle data to projections (e2simmx.py), classification (e2classify.py), the generation of class averages (e2classaverage.py), and finally the generation of a new 3D model (e2make3d.py). This pipeline is depicted graphically in '''Figure 1''' below, along with accompanying data inputs and outputs. || {{attachment:refinepipeline_small.png}} || |
* Direct observation to look for heterogeneity or discover symmetry * Building initial models for single particle reconstruction * Separating particles into subgroups for additional analysis |
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'''Fig. 1. Overview of data inputs and outputs in the EMAN2 refinement pipeline. Pink objects are data supplied by the user, blue objects are programs, and green objects are data output by EMAN2 programs.''' |
This last point can be used to produce 'population-dynamics' movies of a particle in very close to the same orientation. |
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| Most of the command line arguments have defaults, those which are absolutely. The user must atleast specify the total number of iterations, the symmetry and the proportional distribution or number of projections. | ||path||Path to store results||automatic|| |
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|| version || bool || Show program's version number and exit || || h, help || bool || Show help || || c, check || bool || Checks the contents of the current directory to verify that e2refine.py will work || || v, verbose || int || Toggle verbose mode - prints extra infromation to the command line while executing || || input|| string || The input image stack of 2D particles|| || iter|| int|| The number of refinement iterations || || lowmem|| boolean || A low memory flag used to indicate memory should be used as sparsely as possible || || model|| string || The seeding 3D model || || path || string || The directory where output will be stored || || sym|| string|| The [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1Symmetry3D.html|symmetry]] being output 3D models and the limit the range of generated projections || ==== Arguments used to execute e2project3d.py ==== See [[e2project3d|e2project3d.py.]] || orientgen|| string:args || The [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1OrientationGenerator.html|OrientationGenerator]] and parameters used for generation orientations in the asymmetric unit of the 3D model || || projector || string:args || The [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1Projector.html|projector]] used for generating projections || ==== Arguments used to execute e2simmx.py ==== See [[e2simmx|e2simmx.py.]] || shrink || int || The shrink factor applied to particles prior to generation of the similarity matrix (e2simmx.py) || || simalign || string:args || The main [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1Aligner.html|aligner]] used during similarity matrix generation || || simaligncmp || string:args || The [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1Cmp.html|comparator]] used by the main aligner during similarity matrix generation || || simcmp|| string:args || The [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1Cmp.html|comparator]] used to generate the final score which is stored in the similarity matrix || || simralign|| string:args || The refinement [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1Aligner.html|aligner]] used during similarity matrix generation || || simraligncmp || string:args || The [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1Cmp.html|comparator]] used by the refine align in similarity matrix generation || ==== Arguments used to execute e2classify.py ==== See [[e2classify|e2classify.py]] || sep || int || The number of classes each particles can be associated with || ==== Arguments used to execute e2classaverage.py ==== See [[e2classaverage|e2classaverage.py]]. || classalign || string:args || The [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1Aligner.html|aligner]] used for alignment during iterative class averaging || || classaligncmp|| string:args || [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1Cmp.html|Comparator]] used by the main aligner during iterative class averaging || || classaverager|| string::args || [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1Averager.html|Averager]] used for averaging the images in each class || || classcmp || string:args || The main [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1Cmp.html|comparator]] used to quality and exclude bad particles in iterative class averaging || || classiter || int || The number of class averaging iterations || || classkeep|| float || The keep threshold used for excluding bad particles in iterative class averaging || || classnormproc|| string:args || The normalization [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1Processor.html|processor]] used in class averaging || || classralign|| string:args || The refinement [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1Aligner.html|aligner]] used in iterative class averagin || || classraligncmp || string:args || The [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1Cmp.html|comparator]] used by the refinement aligner in iterative class averaging || ==== Arguments used to execute e2make3d.py ==== See [[e2make3d|e2make3d.py.]] || m3diter|| int || The number of iterations used my make3d when performing the Fourier inversion method of 3D reconstruction || || m3dkeep|| float || The keep threshold used by e2make3d for the purpose of slice exclusion during 3D reconstruction || || m3dpreprocess|| string:args || The normalization [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1Processor.html|processor]] applied prior to slice insertion during 3D reconstruction || || pad || int || The amount of padding used by the Fourier inversion 3D reconstruction technique || || recon|| string:args || The [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1Reconstructor.html|reconstructor]] used for performing 3D reconstruction || ==== Arguments used to post process the 3D reconstruction ==== The ByMass links will resolve on January 22 || mass || float || The estimated mass of the particle in kilodalton that, along with the apix argument, is used to run the [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1NormalizeByMassProcessor.html| normalize.bymass processor]] immediately after 3D reconstruction || || apix || float || The physical distance represented by a single pixel. This parameter, along with the mass argument, is used to run the [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1NormalizeByMassProcessor.html| normalize.bymass processor]] immediately after 3D reconstruction. The apix argument is also used for generating the x-axis of the automatically generated convergence plots. || || automask3d || float,int,int,int || The threshold, radius, nshells and nshellsgauss parameters, respectively, of the [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1AutoMask3D2Processor.html| mask.auto3d processor]], which is applied directly after the application of the [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1NormalizeByMassProcessor.html| normalize.bymass processor]]. || <<Anchor(checkfunc)>> === Check functionality === By specifying the --check flag, e2refine.py checks only whether the specified parameters are valid, and nothing more. Example output is shown below. {{{ [someone@localhost]$ e2refine.py --check #### Testing directory contents and command line arguments for e2refine.py Error: you must specify the --it argument start.img contains 2498 images of dimensions 100x100 threed.0a.mrc has dimensions 100x100x100 e2refine.py test.... FAILED #### Test executing projection command: e2project3d.py threed.0a.mrc -f --sym=None --projector=standard --out=e2proj.img --check Error: you must specify one of either --prop or --numproj Error: none is an invalid symmetry type. You must specify the --sym argument e2project3d.py command line arguments test.... FAILED #### Test executing simmx command: e2simmx.py e2proj.img start.img e2simmx.img -f --saveali --cmp=dot:normalize=1 --align=rotate_translate --aligncmp=dot --check --nofilecheck e2simmx.py command line arguments test.... PASSED #### Test executing classify command: e2classify.py e2simmx.img e2classify.img --sep=2 -f --check --nofilecheck e2classify.py command line arguments test.... PASSED #### Test executing classaverage command: e2classaverage.py start.img e2classify.img e2classes.1.img --ref=e2proj.img --iter=3 -f --keepsig=1.000000 --cmp=dot:normalize=1 --align=rotate_translate --aligncmp=phase --check --nofilecheck e2classaverage.py command line arguments test.... PASSED #### Test executing make3d command: e2make3d.py e2classes.1.img --sym=None --iter=4 -f --recon=fourier --out=threed.0a.mrc --keepsig=1.000000 --check --nofilecheck Error: none is an invalid symmetry type. You must specify the --sym argument e2make3d.py command line arguments test.... FAILED }}} This functionality will be useful for people who have to submit their jobs to queues - being able to check that the script will work will ensure its successful execution. |
| Command line arguments | Check functionality | e2refine FAQ |
e2refine2d
e2refine2d.py runs in much the same way as refine2d.py, though it has beein improved in a number of subtle ways in EMAN1
This program will take a set of boxed out particle images and perform iterative reference-free classification to produce a set of representative class-averages. The point of this process is to reduce noise levels, so the overall shape of the particle views present in the data can be better observed. Generally cryo-EM single particles are noisy enough that it is difficult to distinguish subtle, or even not-so-subtle differences between particle images. By aligning and averaging similar particles together, less noisy versions of representative views are created. The class-averages produced by this program are typically used for:
- Direct observation to look for heterogeneity or discover symmetry
- Building initial models for single particle reconstruction
- Separating particles into subgroups for additional analysis
This last point can be used to produce 'population-dynamics' movies of a particle in very close to the same orientation.
Command Line Arguments
path |
Path to store results |
automatic |