![]() The -union option can be used to instad use the union of the two input maps, and -nointerp can be used to turn off interpolation. These commands, except for correlate, have the default behavior of computing the result with the intersection of the two maps and interpolating the values from them. Integral: integral of the map (product of the mean and the volume of all cells). Mean, sigma: mean and standard deviation of the voxel values. Minmax: list containing the minimum and maximum voxel values. Xsize/ysize/zsize: length (number of voxels) of the axis in the given direction. atom's residue is an alpha helix: extendedbeta: bool: atom's residue is a beta sheet: bridgebeta: bool: atom's residue is a beta sheet: rasmol: Rasmol string: translates Rasmol selection syntax to VMD: alphahelix: bool: atom's residue is an alpha helix: pihelix: bool: atom's residue is a pi helix: helix: bool: atom's residue is an alpha or. Origin: x,y,z coordinates of the map's origin.Ĭellaxes: the axes of one individual cell/voxel as a list of lists.Ĭellvolume: the volume of one individual cell/voxel. Gets information about the density map specified by the first argument: info origin | cellaxes | cellvolume | xsize | ysize | zsize | minmax | mean | sigma | integral :.hist :Ĭalculates a histogram of the density map and returns a list of frequencies and bin midpoints.pot :Ĭonvert a density map to an MDFF potential.Write volumetric data to a file (currently. Map that do not fall within the mask and the given cutoff. mask selection :Ĭreates a binary mask around the atom selection by simulating a map of given resolution, then removing all voxels from the input.sim selection :Ĭompute a simulated density map from an atom selection on an all-atom.Which is further away from the atom selection, which can often be noise. The -thresholddensity option ignores voxels with values below x threshold in the simulated density map. Previous message: Peter Freddolino: 'Re: atom selection error' In reply to: Peter Freddolino: 'Re: atom selection error' Messages sorted by: attachment thank you so much for all of your reply. This command uses multi-core CPU and GPU-accelerated algorithms for fast computation, as described in: cc selection :Ĭomputes the MDFF cross correlation between a selection from an all-atom.Structures are ranked according to their cross-correlation score. First, the center of mass of the selection is moved to the center of mass of the density,įollowed by a brute-force rotational search. Performs rigid body fitting of an atom selection to the given density map. Map operations using an atomic structure: The information shows up in the terminal window that VMD produces when you start the program. If you click on an atom, and it appears nothing happens, don’t worry. Output format ( -o filename) must currently be in. To enter query mode, type 0 (that’s a zero) in the display window, or select Mouse.Query from the main VMD menu. The input map format can be any that VMD reads (e.g. With optional -vol volume id which defaults to 0) to avoid unnecessary file i/o. ![]() Maps which have already been loaded into VMD ( -mol molid To load the density map file from disk ( -i filename) or work on The voltool command provides utilities to facilitate the manipulationĪnd analysis of 3D volumetric data (density maps). Next: wait Up: Tcl Text Commands Previous: volmap Contents Index
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