collage - Simultaneous Multi-Fragment Refinement colores - Exhaustive One-At-A-Time 6D Search eul2pdb - Graphical Representation of Euler Angles map2map - Format Conversion matchpt - Point Cloud Matching pdb2sax - Create a Simulated SAXS Bead Model from a PDB pdb2vol - Create a Volumetric Map from a PDB pdbsymm - Symmetry Builder qplasty - Interpolation of Sparsely Sampled Displacements quanpdb - Vector Quantization of a PDB quanvol - Vector Quantization of Volumetric Map vol2pdb - Create a PDB from a Volumetric Map volaver - Map Averaging voldiff - Discrepancy / Difference Mapping voledit - Inspecting 2D Sections and Editing of 3D Maps volfltr - Denoising 3D Maps and 2D Image Stacks volhist - Inspecting and Shifting the Voxel Histogram volmult - Map / Mask Multiplication voltrac - Alpha-Helix Detection and Filament Tracing Header File and Library Routines file3: inputfile 3, Codebook vectors from quanpdb in PDB format. Use NONE if the codebook vectors should be calculated within matchpt file4: inputfile 4, High-resolution structure in PDB format. Use NONE if only the codebook vectors should be matched. file1: inputfile, PDB format file2: outputfile (bead model), PDB format radius: bead radius in Angstrom file1: inputfile, PDB format file2: (optional) inputfile for helical or symmetry axis (density map) file3: outputfile, PDB format file1: inputfile, density map file2: inputfile, start vectors, PDB format (optional) file3: outputfile, PDB format file1: inputfile 1, density map file2: inputfile 2, density map [file...] (optional) additional input maps outfile: outputfile density map Modes: volhist infile1 (print histogram) volhist infile1 outfile (rescale or shift densities) volhist infile1 infile2 outfile (match histogram of infile2 to that of infile1) -lambda <,float>, Orientation-dependent density attenuation parameter (Z vs XY), typically ≤ 1. [default: 1.0] -popsize <,int>, Genetic algorithm population size (increase this number for large maps). [default: 100] -maxgen <,int>, Maximum number of generations explored by the genetic algorithm (this is really only a hard limit of last resort, as the runs are usually stopped early by stop criteria) [default: 10000] -syncgen <,int>, Generations explored before parallel population is synchronized [default: 100] -garadius <,float>, Radius of the search template in Å [default: 2.0] Source.

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