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The resultant trajectories were visualized and analyzed by means of VMD (Visual Molecular Dynamics) software [ 85].
Trajectories were visualized in stereoscopic 3D display to convey spatial and temporal features.
CSΔN and TRAP-VAL sporozoites were imaged 10 and 30 min after intradermal injection into the ear pinna of an anesthetized mouse, and sporozoite trajectories were visualized by maximum intensity projection of the 4-min videos.
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As a quality control measure, each simulation trajectory is visualized using visual molecular dynamics (VMD) and monitored by calculating certain parameters, such as, total energy and the root mean square deviation (RMSD) at regular intervals.
In principal components analysis, the day night plasticity trajectory is visualized.
The fly body and trajectory are visualized by a blue line (white arrow).
Trajectories of these simulations were visualized using VMD v 1.9 (http://www.ks.uiuc.edu/Research/vmd/vmd-1.9/) and the interactions between the kinase and the ligand were plotted using LigPlot+ v 1.4 and PyMol (http://www.schrodinger.com/pymol/).schrodinger.com/pymol/
When the morphology and the trajectory of regrowing axons were visualized in 3D in transparent whole-mounted nerves, very irregular trajectories of single axons and an elevated rate of axonal U-turns were observed.
Trajectories were analyzed using the Ptraj module of AMBER and structures were visualized using the VMD molecular visualization program http://www.ks.uiuc.edu/Research/vmd/ (70).
Although more acrylic balls were visualized with a fixed-tilt and nearly flat cone-beam at the posterior of the breast, 3D complex trajectories have less distortion and more complete sampling throughout the reconstruction volume.
All were visualized.
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