using the cmap function

[nikita chopra]

Hi, Thank you very much for your help regarding the cmap function. I have another question regarding community analysis of Molecular Dynamics trajectory. I am applying the contact map function cmap with distance cutoff of 10 A. I have selected all the CA atoms and my R script is as follows:

pdb<-read.pdb() 
dcd<-read.dcd() 
inds<-atom.select(pdb, elety="CA") 
trj<-fit.xyz(..) 
cm <- cmap(trj, dcut = 10, scut = 0, pcut = 0.75, mask.lower = FALSE)

However, at this step the analysis is terminated in R. Could you please guide me if I am applying the cmap function appropriately ? Thank you again, Nikita

[Lars Skjærven]

Hi Nikita, can you fill out the content of your fit.xyz() function, as well as providing the full error message? That will help to see whats going on.

You might want to checkout the argument grpby for function cmap if your trj variable contains all the atoms. In that case grpby=pdb$resno might be useful.

pdb <- read.pdb() 
dcd <- read.dcd() 
inds <- atom.select(pdb, elety="CA") 
trj <- fit.xyz(..)

# all-atom contact map
cm <- cmap(trj, grpby=pdb$resno, dcut = 10, scut = 0, pcut = 0.75, mask.lower = FALSE)

# calpha contact map
ca.trj <- trj[, inds$xyz, drop=FALSE]
cm <- cmap(ca.trj, dcut = 10, scut = 0, pcut = 0.75, mask.lower = FALSE)

[Xinqiu Yao]

I think I have already answered the same question in another issue #188...

Or, is it actually different question?

[Lars Skjærven]

looks fairly similar to me