Reconstruction Parameters » History » Revision 33
Revision 32 (Amber Herold, 05/31/2011 03:23 PM) → Revision 33/37 (Amber Herold, 05/31/2011 03:24 PM)
h1. Reconstruction Parameters |_.Name|_.a.k.a.|_.Description|_.Used By|_.Make common to all?|_.Notes| |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| |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| ||||||| |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 |firstring||Any pixels this far away from center will not be used|spider||| |lastring|similar to alignment radius|Only |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||| |angular increments||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|||