![]() ![]() density: unit of the density if isDensity=True or None.length: physical unit of grid edges (Angstrom or nm).False: grid is a histogram with counts Īpplying Density.make_density`() sets it to True.Supplying an AtomGroup, then use the run() method: , first create the DensityAnalysis object by The trajectory is already appropriately treated for periodic boundaryĪrtifacts and is suitably superimposed to provide a fixed reference frame) To generate the density of water molecules around a protein (assuming that Protein on a reference structure so that one can study the solvent have a fixed frame of reference for instance, by superimposing a.Solvent will appear in the reference frame of the protein.Ī dodecahedron or a truncated octahedron) Other components of the simulation with the protein. In practice this means centering and superimposing the protein,įrame by frame, on a reference structure and translating and rotating all Necessary to orient and fix the protein with respect to the box coordinate The density is calculated with DensityAnalysis in theįixed coordinate system of the simulation unit cell. If you want dynamically changing selections (such as “name OW andĪround 4.0 (protein and not name H*)”, i.e., the water oxygen atoms thatĪre within 4 Å of the protein heavy atoms) then create an Normal AtomGroup instances represent a static selection ofĪtoms. zdim ( float ( optional )) – User defined z dimension box edge in ångström ignored if.ydim ( float ( optional )) – User defined y dimension box edge in ångström ignored if.xdim ( float ( optional )) – User defined x dimension box edge in ångström ignored if.gridcenter ( numpy ndarray, float32 ( optional )) – 3 element numpy array detailing the x, y and z coordinates of theĬenter of a user defined grid box in ångström.Padding is ignored when setting a user defined padding ( float ( optional )) – Increase histogram dimensions by padding (on top of initial box.delta ( float ( optional )) – Bin size for the density grid in ångström (same in x,y,z).atomgroup ( AtomGroup or UpdatingAtomGroup) – Group of atoms (such as all the water oxygen atoms) being analyzed.Histogrammed on a 3D grid with spacing delta. The trajectory is read, frame by frame, and the atoms in atomgroup are ![]() DensityAnalysis ( atomgroup, delta=1.0, metadata=None, padding=2.0, gridcenter=None, xdim=None, ydim=None, zdim=None ) ¶ The crystallographic temperature factors (B-factor) with Bfactor2RMSF(). Replacing each atom with a Gaussian density with a width that is computed from Its function equivalent density_from_Universe() is deprecated.ĭensity_from_PDB() generates a pseudo-density from a PDB file by The DensityAnalysis class generates a Density from anĪtomgroup. ![]() Is suitably superimposed to provide a fixed reference frame) Trajectory is already appropriately treated for periodic boundary artifacts and To generate the density of water molecules around a protein (assuming that the On a reference structure so that one can study the solvent density around
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