Time consuming network analysis

[Aiswarya Pawar]

Hi ,

I was using the network analysis module, to perform it on 170 amino acid length protein, with 5000 frames. I tried by giving the contact map with a cut off, but in this step the analysis gets stuck and runs forever, shows 0% for a long time. Am running it on a macbook i5. Does it require an additional computing power? Below is the commands i have used.

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library(bio3d)

library(igraph)

pdb <- read.pdb('temp.pdb')

dcd <- read.dcd('temp.dcd')

inds <- atom.select(pdb, resno = c(24:38), elety = "calpha")

trj <- fit.xyz(fixed = pdb$xyz, mobile = dcd,fixed.inds = inds$xyz, mobile.inds = inds$xyz)

cm <- cmap.xyz(trj,dcut=0.5, scut=0, pcut=0.75, mask.lower=FALSE,ncore=4, gc.first=TRUE)

[Xinqiu Yao]

Hi,

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You may need to provide a grpby to the call; otherwise, it will calculate contacts for all atoms (which is very large and so slow down).

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For example, try cmap(trj, grpby=pdb$atom$resno, ...)