Appion

h1. 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|

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|_.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|||

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|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|||