geometry - measure various molecular geometry.frame_rmsd - computes rmsd between two frames of a trajectory.trajectory_path - Draws the path of the center of mass of a selection through an animation.stride_workaround - Works around a limitation in STRIDE, allowing determination of secondary structure of proteins in very large structures.metal_environment - Finds the propensity of residues near given ions.HOLE - a script for running the HOLE program written by Oliver Smart.ColorCoord - set residue user field according to number of hbonds formed with neighbors.ca-dist - Given a selection, plot the CA-CA distance.bigdcd - Analyze large Charmm/X-PLOR/NAMD "DCD" trajectories.mono2poly - Build complete biological unit from PDB BIOMT records.mergepdbs - Merge several PDB files together into a single structure using the psfgen plugin.splitmultiframepdb - Split multi-frame NMR structures into separate molecules and load them into VMD.mergemultiframepdb - Merge large multi-frame virus capsid structures into a single structure using the psfgen plugin.Tcl VMD scripts Structure building scripts selpath - draws a trace through the average position of an atom selection over a trajectory.reswin - sequence selection and coloring script.fit_angle - finds the angle between the best-fit line through two selections or a given vector. The Tcl and Python scripting sections in the If you would like to learn more about these scripts, you can read More general-purpose use, though some of them may serve your needs as-is. Scripts perform a very specific task, and would need to be modified for The scripts provided here are relatively simple examples of what canīe done using the scripting interfaces in VMD. Procedure definitions, and many other features. Loops, variable substitution, if-then-else constructs, function and This allows scripts to be written which can load molecules, make movies, Most VMD functions can be accessed through text commands implemented
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