Differential RMSF

[Former user]

Hi,

I would like to know how can we tweak the code for the differential rmsf. For a normal rmsf of independent simulations ex: sim1, sim2, sim3. i can do something like this:

ca.inds <- atom.select(pdb, elety = 'CA')
xyz1 <- fit.xyz(fixed=pdb$xyz,mobile=trj1,fixed.inds=ca.inds$xyz,mobile.inds=ca.inds$xyz)
sim1 <- rmsf(xyz1 [,ca.inds$xyz])
xyz2 <- fit.xyz(fixed=pdb$xyz,mobile=trj2,fixed.inds=ca.inds$xyz,mobile.inds=ca.inds$xyz)
sim2 <- rmsf(xyz2 [,ca.inds$xyz])
xyz3 <- fit.xyz(fixed=pdb$xyz,mobile=trj3,fixed.inds=ca.inds$xyz,mobile.inds=ca.inds$xyz)
sim3 <- rmsf(xyz3 [,ca.inds$xyz])

plot(sim1,typ="l",lwd=2,col="#E16A86")
points(sim2,typ="l",lwd=2,col="#B88A00")
points(sim3,typ="l",lwd=2,col="#50A315")

But if i want to look at how much the rmsf is deviate sim2 and sim3 with respect to sim1. how do i tweak the current code. and will i be able to write out mktrj from this differential value, the same way we write out normal rmsf.?

[Aiswarya Pawar]

ok i just took the diff,

sim<-sim1-sim2 and did get the plot.

But how do i get those values into pdb using mktrj command?

[Xinqiu Yao]

Hi,

You can put RMSF values in the “b-factor” column of PDB and then view them with different colors provided by VMD for example. The command you may use is write.pdb(pdb,"file=”myfi"e.pdb”, b=sim)