|
Size: 1211
Comment:
|
Size: 3559
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 2: | Line 2: |
| == Description == Note: Despite the experimental tags, the 'phasecls' and 'fscls' almost always produce better results than the default linear variance classifier. Note that these options are mutually exclusive. |
|
| Line 5: | Line 3: |
| This is the main refinement command in EMAN. You should have your starting images in 'start.img' and your initial 3D model in threed.0a.mrc. The 'refine' command will then refine this model iteratively. Note that the 'total number of iterations' specifies the number of iterations the program will finish with. If 5 iterations have been run, then 'refine 8 ...' is run, the program will pick up after 5 iterations and run only 3 more cycles. If you want to start over again from the first iteration, you must remove all of the 'threed.?.mrc' files (except for 0a) and all of the 'classes.?.mrc' files. | ''There are over 200 command-line programs in EMAN, this list contains more detailed documentation for the most commonly used programs. See the fixed documentation for a full list.'' |
| Line 7: | Line 5: |
| Most of the options are simply passed through to other programs. Typical options for this program can be determined by running [/eman/eman1/progs/eman.html eman] and following the reconstruction procedure it provides. | '''GUI Programs''' ||[wiki:/Eman eman]||Image browser and tutorial interface|| ||[wiki:/Boxer boxer]||Manual particle picking|| ||[wiki:/CTFit ctfit]||CTF parameter determination and simulation|| ||[wiki:/V4 v4]||Viewing 3-D models in projection|| ||[wiki:/QSegment qsegment]||Interactive slice-by-slice 3D model segmentation|| ||[wiki:/QIndex qindex]||2D crystal preprocessing and evaluation|| ||[wiki:/HelixBoxer helixboxer]||Program for picking and evaluating non-square 'boxes'|| |
| Line 9: | Line 14: |
| The tree option may not work in certian parallel configurations, such as grid configurations where the filesystem isn't cross-mounted. | '''Refinement Programs''' ||[wiki:/Refine2D refine2d.py]||Make high-quality 2-D class-averages from stacks of raw particle images|| ||[wiki:/Refine refine]||3-D model refinement|| ||[wiki:EoTest eotest]||Even/odd data split for resolution evaluation after refinement|| ||[wiki:/MultiRefine multirefine]||Simultaneous multiple model 3-D refinement|| '''Utility Programs''' ||[wiki:/Proc2D proc2d]||Generic 2-D image processing|| ||[wiki:/Proc3D proc3d]||Generic 3-D image processing|| ||[wiki:/ProcPDB procpdb.py]||Simple PDB file manipulation|| ||[wiki:/ImInfo iminfo]||Dump information about image files|| ||[wiki:/SpeedTest speedtest]||Simple application-specific computer benchmarking program|| ||[wiki:LstCat lstcat.py]||Generate pseudoimage text files|| ||[wiki:LstFast lstfast.py]||Optimize pseudoimage files for rapid access|| ||[wiki:PdbToMrc pdbtomrc]||Convert PDB files to MRC density maps|| ||[wiki:Align2D align2d]||Align 2-D particles to a common reference|| ||[wiki:Align3D align3d]||Aligns a 3-D model to a similar 3-D model|| ||[wiki:Align3DSym align3dsym||Align a 3-D model so symmetry axes are along canonical axes|| ||[wiki:Volume volume]||Compute or adjust the volume of a 3-D reconstruction|| '''Refinement-related Processing''' ||[wiki:/BatchBoxer batchboxer]||Command-line automatic particle picking and box manipulation|| ||[wiki:/FitCtf fitctf]||Automatic CTF parameter determination|| ||[wiki:/ApplyCtf applyctf]||Perform phase flipping and other CTF-correction operations|| ||[wiki:/SfMerge sfmerge.py]||Merge a low resolution 1-D structure factor from ctfit with a high resolution solution scattering curve|| ||[wiki:MakeInitialModel makeinitialmodel.py]||Interactive script for generating initial models out of Gaussian blobs|| ||[wiki:StartCSym startcsym]||Generate initial models from data with Cn and Dn symmetries|| ||[wiki:StartIcos starticos]||Generate initial models from data with icosahedral (532) symmetry|| ||[wiki:StartOct startoct]||Generate an initial model from data with octahedral (432) symmetry|| ||[wiki:StartAny startAny]||Initial model generation using common-lines. Usually a bad idea...|| ||[wiki:PtclTrace ptcltrace]||Observe particle orientation changes during refinement|| ||[wiki:Segment3D segment3d]||Automatic segmentation of 3-D reconstructions|| '''AIRS Tools (Analysis of Intermediate Resolution Structures)''' ||[wiki:/FoldHunter foldhunter.py]||Dock a PDB file or density segment in a 3-D reconstruction|| ||[wiki:/SseHunter ssehunter.py]||Identify/locate secondary structural elements in subnanometer resolution reconstructions|| ||[wiki:/HelixHunter helixhunter.py]||Program to locate alpha-helices in subnanometer resolution reconstructions|| ||[wiki:/Skeleton skeleton]||Skeletonization of 3-D models based on both lines and planes|| |
EMAN1 Individual Programs
There are over 200 command-line programs in EMAN, this list contains more detailed documentation for the most commonly used programs. See the fixed documentation for a full list.
GUI Programs
[wiki:/Eman eman] |
Image browser and tutorial interface |
[wiki:/Boxer boxer] |
Manual particle picking |
[wiki:/CTFit ctfit] |
CTF parameter determination and simulation |
[wiki:/V4 v4] |
Viewing 3-D models in projection |
[wiki:/QSegment qsegment] |
Interactive slice-by-slice 3D model segmentation |
[wiki:/QIndex qindex] |
2D crystal preprocessing and evaluation |
[wiki:/HelixBoxer helixboxer] |
Program for picking and evaluating non-square 'boxes' |
Refinement Programs
[wiki:/Refine2D refine2d.py] |
Make high-quality 2-D class-averages from stacks of raw particle images |
[wiki:/Refine refine] |
3-D model refinement |
[wiki:EoTest eotest] |
Even/odd data split for resolution evaluation after refinement |
[wiki:/MultiRefine multirefine] |
Simultaneous multiple model 3-D refinement |
Utility Programs
[wiki:/Proc2D proc2d] |
Generic 2-D image processing |
[wiki:/Proc3D proc3d] |
Generic 3-D image processing |
[wiki:/ProcPDB procpdb.py] |
Simple PDB file manipulation |
[wiki:/ImInfo iminfo] |
Dump information about image files |
[wiki:/SpeedTest speedtest] |
Simple application-specific computer benchmarking program |
[wiki:LstCat lstcat.py] |
Generate pseudoimage text files |
[wiki:LstFast lstfast.py] |
Optimize pseudoimage files for rapid access |
[wiki:PdbToMrc pdbtomrc] |
Convert PDB files to MRC density maps |
[wiki:Align2D align2d] |
Align 2-D particles to a common reference |
[wiki:Align3D align3d] |
Aligns a 3-D model to a similar 3-D model |
[wiki:Align3DSym align3dsym |
Align a 3-D model so symmetry axes are along canonical axes |
[wiki:Volume volume] |
Compute or adjust the volume of a 3-D reconstruction |
Refinement-related Processing
[wiki:/BatchBoxer batchboxer] |
Command-line automatic particle picking and box manipulation |
[wiki:/FitCtf fitctf] |
Automatic CTF parameter determination |
[wiki:/ApplyCtf applyctf] |
Perform phase flipping and other CTF-correction operations |
[wiki:/SfMerge sfmerge.py] |
Merge a low resolution 1-D structure factor from ctfit with a high resolution solution scattering curve |
[wiki:MakeInitialModel makeinitialmodel.py] |
Interactive script for generating initial models out of Gaussian blobs |
[wiki:StartCSym startcsym] |
Generate initial models from data with Cn and Dn symmetries |
[wiki:StartIcos starticos] |
Generate initial models from data with icosahedral (532) symmetry |
[wiki:StartOct startoct] |
Generate an initial model from data with octahedral (432) symmetry |
[wiki:StartAny startAny] |
Initial model generation using common-lines. Usually a bad idea... |
[wiki:PtclTrace ptcltrace] |
Observe particle orientation changes during refinement |
[wiki:Segment3D segment3d] |
Automatic segmentation of 3-D reconstructions |
AIRS Tools (Analysis of Intermediate Resolution Structures)
[wiki:/FoldHunter foldhunter.py] |
Dock a PDB file or density segment in a 3-D reconstruction |
[wiki:/SseHunter ssehunter.py] |
Identify/locate secondary structural elements in subnanometer resolution reconstructions |
[wiki:/HelixHunter helixhunter.py] |
Program to locate alpha-helices in subnanometer resolution reconstructions |
[wiki:/Skeleton skeleton] |
Skeletonization of 3-D models based on both lines and planes |