PCA, RMSD, RMSF plot

[Former user]

Hey.. I am using Bio3D to get the RMSD, RMSF and PCA graphs. I am using my own molecules(4 molecules) for which I did equilibration and production using NAMD and ACEMD. I did tutorial for each molecule. I would like to know how could I get one RMSD graph, one RMSF graph and one PCA graph for all four molecules together? Thank You in advance, Luana.

[Xinqiu Yao]

Generally, you should be able to group figures using the layout() function (See help(layout) for more detail). Also, each function may have a specific way to plot multiple lines (e.g., plot.fluct()). What functions exactly did you make those figures?

[luanacro]

Hey.. I have been using this tutorial http://thegrantlab.org/bio3d/tutorials/trajectory-analysis and all commands I have used are from this tutorial. Thank You on Yours reply.

[Xinqiu Yao]

Not a bug.

[Xinqiu Yao]

For RMSD you should be able to put lines together using the basic R function plot() and then lines().

For RMSF, there is a function called plot.fluct() in bio3d that allows you to plot lines for multiple systems.

You have to do a PCA taking all simulations together, and then plot them on one graph. You can color frames of different molecules with different colors, if simulation trajectories are simply concatenated.

Hope it helps.