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Reconstruction Parameters » History » Version 7

Amber Herold, 05/31/2011 12:35 PM

1 1 Amber Herold 
h1. Reconstruction Parameters
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|_.Name|_.a.k.a.|_.Description|_.Used By|_.Required in interface?|





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





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





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





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|Outer Radius|||xmipp||





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





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





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





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





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|Mask Filename|||xmipp||





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





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|Angular Sampling Rate|||xmipp||





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|Max angular change|||xmipp||





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|max change offset|||xmipp||





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





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





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|Reconstruction Method|||xmipp||





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





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





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|Compute resolution?|||xmipp||





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





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





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





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





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





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





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|hard||hard limit for make3d program|eman||





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|clskeep||=[std dev multipier] how many raw particles discarded for each class average|eman||





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|clsiter||iterative alignmnet to each other|eman||





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





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





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|Approximate mass in Kd |||imagic||





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|shrink||scale down by a factor of [n] before classification|eman||





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|euler2||=[oversample factor]|eman||





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|median||use median value instead of average for each pixel|eman||





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|phscls||use signal to noise ratio weighted phase residual|eman||





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|refine||do subpixel alignment|eman||





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|tree||decimate reference populatiuon|eman||





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|coran||use coran algorithm|eman||





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|eotest||use even odd test|eman||





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





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|Standard deviation filtering|||fealign||





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





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|Phase B-factor weighting constant (PBC) |||frealign||





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|B-factor offset (BOFF) |||frealign||





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|Number of randomized search trials (ITMAX) |||frealign||





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|Number of potential matches to refine (IPMAX)|||frealign||





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|Target phase residual (TARGET) |||frealign||





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|Worst phase residual for inclusion (THRESH)|||frealign||





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|Resolution limit of reconstruction (RREC) (in Ångstroms; default Nyquist) |||frealign||





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





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





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





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





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





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|Only use CTFFIND values|||frealign||





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|Last particle to use|||frealign||





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





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|lastring||Only pixels this far away will be used|spider||





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|xysearch|||spider||





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





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





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





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





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





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





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





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|MSA - num class averges to produce from raw images|||imagic||





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|MSA - num factors to use for classification|||imagic||





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|MSA - percentage of worst class members to ignore after classification|||imagic||





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





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|threed reconstruction||object size, low-pass filter 3d volume|imagic||





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|Center stack prior to alignment |||imagic||





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|Mirror references for alignment |||imagic||