- edited description
using the cmap function
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
Comments (4)
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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)
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I think I have already answered the same question in another issue
#188...Or, is it actually different question?
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- changed status to resolved
looks fairly similar to me
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