PCA, RMSD, RMSF plot
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.
Comments (5)
-
-
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.
-
Not a bug.
-
For RMSD you should be able to put lines together using the basic R function
plot()
and thenlines()
.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.
-
- changed status to resolved
- Log in to comment
Generally, you should be able to group figures using the
layout()
function (Seehelp(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?