Extract PDBs that represent the normal modes

[Rebecca Alford]

Hello,

I apologize in advance if this question is redundant. How can I extract PDB files that represent the motions due to the different normal modes? I am able to visualize the vector field in PyMOL. How can I get the individual structures, such as in the left side of Figure 3 in the Normal Modes tutorial (Page 7 in the PDF for GroEL). I am familiar with PyMOL but not as familiar with other trajectory analysis tools such as VMD.

thanks,

Rebecca

[Xinqiu Yao]

Take a look of the mktrj() function, which outputs a mode into a PDB file containing several structural snapshots. Then, you can use VMD or PyMol to open the PDB file and make a similar plot as shown in the tutorial. Hope it helps.