how to get the protein structure with PC values projection on trajectory

[Former user]

in the Principal Component Analysis section of your tutoial (Beginning Trajectory Analysis with Bio3D), there is a HIV-1 protease strucutre ( Visualization of the first principal component of HIV-1 protease. Color scale from blue to red depict low to high atomic displacements.). I follow your instruciton ( To view the PDB trajectories in VMD just open the files in the normal way and display as tube representation. but I did not get the protein struture figure as your example. Could you help to how get the strucure as your example? TAHNKS.

[Xinqiu Yao]

The atomic displacement information is saved in the “B factor” column of the PDB file. To show them, color the protein by “Beta” in VMD. You may also need to change the direction of the color scale, which is under ‘Graphics → Colors’ menu. To show the trajectory in one view, check ‘Trajectory’ and set proper values in ‘Draw Multiple Frames’. Note that all are related to the VMD software. For more detail, please check their manual/tutorials: https://www.ks.uiuc.edu/Research/vmd/

[Xinqiu Yao]

Not a bug.