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.