Only lines that start with one of theĪbove field names are evaluated by NMWiz. bfactors: list of experimental beta-factors If not provided, all beta-factors are set to zero.īeta-factors can be used to color the protein representation. resids: list of residue numbers If not provided, residue numbers are started from 1 and incremented by oneįor each atom. chainids: list of chain identifiers If not provided, all chain identifiers are set to “A”. resnames: list of residue names If not provided, all residue names are set to “GLY”. atomnames: list of atom names If not provided, all atom names are set to “CA”. NMWiz uses such data when writing a temporary PDB files for The length of all following data fields must be equal to the number of atoms in Mode 2.37 0.039 0.009 0.058 0.038 -0.011 0.052. Some programs that are useful for visualizing either a trajectory file and/or a coordinate file are: VMD - a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. Mode 1 2.37 0.039 0.009 0.058 0.038 -0.011 0.052. In the Assets menu, tap import icon, then you will see a document selection view. Second and third lines contain mode index or If data is from an elastic network model, or the square-root of theĮigenvalue if data is from an essential dynamics (or principal component)įor example, all of the following lines are valid. Scaling factor may be the square-root of the inverse eigenvalue If a decimal number is encountered, it is considered the scalingįactor. If an integer is encountered, it is considered the mode If a mode line contains numbers preceding the mode array, they are evaluatedīased on their type. Analogously, for PCA data, scaling factor would be the May be chosen to be the square-root of the inverse-eigenvalue associated The amplitude of the fluctuations in animations. Providing a scaling factor enables relative scaling of the mode arrows and Both of these must precede the mode array. Optionally, mode index and a scaling factor may be provided Mode: normal mode array as a list of decimal numbers
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