Reconstruction Parameters » History » Revision 4
Revision 3 (Amber Herold, 05/31/2011 12:07 PM) → Revision 4/37 (Amber Herold, 05/31/2011 12:15 PM)
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|| eman|| |Inner Radius||inner radius for alignment in pixels|xmipp|| |imask|Particle inner mask raduius|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|| |Symmetry Group|sym|ex. c1, c2...|xmipp,eman,frealign,spider,imagic|| c2...|xmipp,eman,frealign,spider|| |Number of iterations|iteration number||xmipp|| |Mask Filename|||xmipp|| |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|| |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|| |filt3d||applies gaussian low pass filter in pixels [rad]|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|| |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|| |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|| |firstring||Any pixels this far away from center will not be used|spider|| |lastring||Only pixels this far away will be used|spider|| |xysearch|||spider|| |lp|filtering|low |lp||low pass filter in angstroms|spider, imagic|| angstroms|spider|| |hp|filtering|high |hp||high pass filter in angstroms|spider, imagic|| angstroms|spider|| |xyshift||particles only allowed to shift this far from center|spider|| |keep||determines which particles are kept for back-projection, -1 is one standard deviation worse than mean|spider|| |angular increments||list of angular increments for projection mapping|spider|| |MRA||multi-reference alignment of raw particles params|imagic|| |MSA||multi-variate statistical analysis params|imagic|| |Angular reconstitution||angular increment of forward projections, ang inc of euler search, fraction of best ordered images to keep|imagic|| |threed reconstruction||object size, low-pass filter 3d volume|imagic|| |Approximate mass in Kd |||imagic|| |Center stack prior to alignment |||imagic|| |Mirror references for alignment |||imagic||