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Reconstruction Parameters¶
| Name | a.k.a. | Description | Used By | Make common to all? | Notes |
|---|---|---|---|---|---|
| General Refinement Parameters | |||||
| Outer Mask Radius | Particle outer mask radius (RO),Outer Radius, mask | radius from center of particle to outer edge (frealign in angstroms, spider in pixels), raduius of external map in pixels | frealign, spider,xmipp, eman, imagic | y | |
| Inner Mask Radius | Inner Radius,Particle inner mask radius | inner radius for alignment in pixels | xmipp, frealign, spider | y | not xmipp |
| Outer Alignment Radius | xmipp, eman, imagic | y | not eman, frealign | ||
| Inner Alignment Radius | xmipp, eman, imagic | y | not eman, frealign | ||
| Symmetry Group | sym | ex. c1, c2... | xmipp,eman,frealign,spider,imagic | y | |
| Number of iterations | iteration number | xmipp | y | ||
| Angular Sampling Rate | ang | angular step for projections in degrees | xmipp,EMAN | y | not frealign |
| Percentage of worst images to discard | xmipp | y | not frealign | ||
| Filter reconstructed volume to estimated resolution | flt3d | y | not frealign | ||
| Filter reconstructed volume to resolution computed by fsc | Low Pass Filter the reference?, Constant to add to the estimated resolution | y | not frealign, eman | ||
| stack preparation parameters | |||||
| Last particle to use | frealign | y | specific to stack preparation, not refinement alg | ||
| lp | filtering | low pass filter in angstroms | spider, imagic | y | specific to stack preparation, not refinement alg |
| hp | filtering | high pass filter in angstroms | spider, imagic | y | specific to stack preparation, not refinement alg |
| Algorithm Specific Refinement Parameters | |||||
| imask | radius of internal mask (in pixels for eman and spider, Angstroms for frealign) | EMAN | |||
| amask | amask=[r],[threshold],[iter] | eman | |||
| Mask Filename | xmipp | ||||
| Max angular change | xmipp | ||||
| max change offset | xmipp | ||||
| Search range for 5d transitional search | xmipp | ||||
| Reconstruction Method | xmipp | ||||
| Values of lambda for ART | xmipp | ||||
| Initial max frequency used by reconstruct fourier | xmipp | ||||
| Compute resolution? | xmipp | don't need this, should always be set to yes | |||
| maxshift | max translation during image alignment in pixels | eman | |||
| hard | hard limit for make3d program | eman | |||
| clskeep | =[std dev multipier] how many raw particles discarded for each class average | eman | |||
| clsiter | iterative alignmnet to each other | eman | |||
| xfiles | =[mas in kD] | eman | |||
| shrink | scale down by a factor of [n] before classification | eman | |||
| euler2 | =[oversample factor] | eman | |||
| median | use median value instead of average for each pixel | eman | |||
| phscls | use signal to noise ratio weighted phase residual | eman | |||
| refine | do subpixel alignment | eman | |||
| tree | decimate reference populatiuon | eman | |||
| coran | use coran algorithm | eman | |||
| eotest | use even odd test | eman | remove this, should always be yes, takes place of Compute Resolution? | ||
| amplitude contrast (WGH) | frealign | ||||
| Standard deviation filtering | fealign | ||||
| Phase B-factor weighting constant (PBC) | frealign | ||||
| B-factor offset (BOFF) | frealign | ||||
| Number of randomized search trials (ITMAX) | frealign | ||||
| Number of potential matches to refine (IPMAX) | frealign | ||||
| Target phase residual (TARGET) | frealign | ||||
| Worst phase residual for inclusion (THRESH) | frealign | ||||
| Resolution limit of reconstruction (RREC) (in Ångstroms; default Nyquist) | frealign | ||||
| Lower resolution limit or high-pass filter (RMAX1) (in Ångstroms) | frealign | ? is this the same as stack prep lp/hp filter | |||
| Higher resolution limit or low-pass filter (RMAX2) (in Ångstroms; default 2*Nyquist) | frealign | ? is this the same as stack prep lp/hp filter | |||
| B-factor correction (RBFACT) (0 = off) | frealign | ||||
| Only use CTFFIND values | frealign | ||||
| MSA - num class averges to produce from raw images | imagic | ||||
| MSA - num factors to use for classification | imagic | ||||
| MSA - percentage of worst class members to ignore after classification | imagic | ||||
| threed reconstruction | object size, low-pass filter 3d volume | imagic | |||
| Center stack prior to alignment | imagic | ||||
| Mirror references for alignment | imagic | ||||
| MRA - min radius for rotational alignment in pixels | imagic | ||||
| MRA - max radius for rotational alignment in pixels | imagic | ||||
| MSA - fraction of final class averages to keep | imagic | ||||
| MRA - angular increment of forward projections | imagic | ||||
| MRA - max radial shift compared to original images | imagic | ||||
| MRA - max radial shift during this iteration | imagic | ||||
| MSA - percentage of images to ignore when calculating eiganimages | imagic | ||||
| Angular reconstitution | angular increment of forward projections, ang inc of euler search, fraction of best ordered images to keep | imagic | |||
| firstring | similar to alignment radius | Any pixels this far away from center will not be used | spider | ||
| lastring | similar to alignment radius | Only pixels this far away will be used | spider | ||
| xysearch | translational search during projection matching will be limited to this many pixels from the center ofthe image | spider | |||
| angular increments | Angular Sampling Rate | list of angular increments for projection mapping | spider | ||
| keep | determines which particles are kept for back-projection, -1 is one standard deviation worse than mean | spider | |||
| xyshift | particles only allowed to shift this far from center | spider | |||
| Approximate mass in Kd | imagic |
Updated by Amber Herold almost 13 years ago · 37 revisions