Appion

h1. Reconstruction Parameters

|_.Name|_.a.k.a.|_.Description|_.Used By|_.Required in interface?|

|Mask Radius|mask|raduius of external map in pixels|xmipp, eman, imagic||

|Inner Radius||inner radius for alignment in pixels|xmipp||

|imask|Particle inner mask radius|radius of internal mask (in pixels for eman and spider, Angstroms for frealign)|EMAN, frealign, spider||

|Outer Radius|||xmipp||

|Particle outer mask radius (RO)|mask|radius from center of particle to outer edge (frealign in angstroms, spider in pixels)|frealign, spider||

|amask||amask=[r],[threshold],[iter]|eman||

|MRA - min radius for rotational alignment in pixels|||imagic||

|MRA - max radius for rotational alignment in pixels|||imagic||

|firstring||Any pixels this far away from center will not be used|spider||

|lastring||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||

|Symmetry Group|sym|ex. c1, c2...|xmipp,eman,frealign,spider,imagic||

|Number of iterations|iteration number||xmipp||

|Mask Filename|||xmipp||

|Angular reconstitution||angular increment of forward projections, ang inc of euler search, fraction of best ordered images to keep|imagic||

|Angular Sampling Rate|||xmipp||

|Max angular change|||xmipp||

|max change offset|||xmipp||

|Search range for 5d transitional search|||xmipp||

|Discard % of image with CCF below|||xmipp||

|Reconstruction Method|||xmipp||

|Values of lambda for ART|||xmipp||

|Initial max frequency used by reconstruct fourier|||xmipp||

|Compute resolution?|||xmipp||

|Low Pass Filter the reference?|||xmipp||

|Do not use estimated resolution for low-pass filtering?|||xmipp||

|Constant to add to the estimated resolution|||xmipp||

|ang||angular step for projections in degrees|EMAN||

|angular increments||list of angular increments for projection mapping|spider||

|MRA - angular increment of forward projections|||imagic||

|maxshift||max translation during image alignment in pixels|eman||

|xyshift||particles only allowed to shift this far from center|spider||

|MRA - max radial shift compared to original images|||imagic||

|MRA - max radial shift during this iteration|||imagic||

|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||

|filt3d||applies gaussian low pass filter in pixels [rad]|eman||

|xfiles||=[mas in kD]|eman||

|Approximate mass in Kd |||imagic||

|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||

|amplitude contrast (WGH)|||frealign||

|Standard deviation filtering|||fealign||

|keep||determines which particles are kept for back-projection, -1 is one standard deviation worse than mean|spider||

|MSA - fraction of final class averages to keep|||imagic||

|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||

|lp|filtering|low pass filter in angstroms|spider, imagic||

|hp|filtering|high pass filter in angstroms|spider, imagic||

|Lower resolution limit or high-pass filter (RMAX1) (in Ångstroms) |||frealign||

|Higher resolution limit or low-pass filter (RMAX2) (in Ångstroms; default 2*Nyquist) |||frealign||

|B-factor correction (RBFACT) (0 = off)|||frealign||

|Only use CTFFIND values|||frealign||

|Last particle to use|||frealign||

|MSA - percentage of images to ignore when calculating eiganimages|||imagic||

|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||