suboptimal path analysis visualization

[jhold]

In addition to viewing the suboptimal path in VMD...is it feasible to generate a plot of the residues involved in the path?

Unfortunately I tried plot(pa, pdb)

this did not return a result. Any suggestions?

[Xinqiu Yao]

Try summary() or print(pa, pdb, plot=TRUE).

[jhold]

Doing so gives the following error message:

Error in summary.cnapath(x, ...) : Input should be object(s) of the 'cnapath' class

[Xinqiu Yao]

Is the input pa directly obtained from cnapath()? Can you check its class by class(pa)? Also, what bio3d version did you use?

[jhold]

Yes, input pa is obtained from cnapath.

class(pa) = [1] "function"

I have 2.3-3

[Xinqiu Yao]

The 'pa' might have been overwritten by another object - the proper class should be 'cnapath' not 'function'. Could you check your script to see if the same variable name is reused somewhere?

Also, how did you calculate 'pa' exactly? (Paste the command of calling 'cnapath()' here please).

[jhold]

I've copy/pasted by script below. Again, thank you for your help troubleshooting this!

library(bio3d) setup.ncore(2)

dcd <- read.dcd(mydcdfile) pdb <- read.pdb(mypdbfile)

ca.inds <- atom.select(pdb, elety="CA") xyz <- fit.xyz(fixed=pdb$xyz, mobile=dcd, fixed.inds=ca.inds$xyz, mobile.inds=ca.inds$xyz) dim(xyz) == dim(dcd)

cij<-dccm(xyz[,ca.inds$xyz]) net <- cna(cij, cutoff.cij=0.5) x <- summary(net)

library(igraph) modes <- nma(pdb)

node.betweenness <- betweenness(net$network)

pa <- cnapath(net, from=185, to=31, k=50) vmd.cnapath(pa, spline=TRUE, col="cyan", clean.pdb(pdb), fix.chain=TRUE, launch = TRUE) print(pa, label="XXX", plot=TRUE) print(pa, pdb, plot=TRUE) summary(pa, pdb, plot=TRUE)

[jhold]

lets retry with better spacing...

library(bio3d)

setup.ncore(2)

dcd <- read.dcd(mydcdfile)

pdb <- read.pdb(mypdbfile)

ca.inds <- atom.select(pdb, elety="CA")

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

dim(xyz) == dim(dcd)

cij<-dccm(xyz[,ca.inds$xyz])

net <- cna(cij, cutoff.cij=0.5)

x <- summary(net)

library(igraph)

modes <- nma(pdb)

node.betweenness <- betweenness(net$network)

pa <- cnapath(net, from=185, to=31, k=50)

vmd.cnapath(pa, spline=TRUE, col="cyan", clean.pdb(pdb), fix.chain=TRUE, launch = TRUE)

print(pa, label="XXX", plot=TRUE)

print(pa, pdb, plot=TRUE)

summary(pa, pdb, plot=TRUE)

[Xinqiu Yao]

Hi,

I only spotted one minor error in your codes - clean.pdb(pdb), fix.chain=TRUE should be clean.pdb(pdb, fix.chain=TRUE) (Note the position of parenthesis). But I don't think this is related to the problem you reported above.

From the codes, I don't see the reason causing the problem. Could you provide example data that we can reproduce the error? For example, you can save the 'net' and 'pdb' objects in a binary .RData file (see help(save) for more detail) and attach it here or send it to [e-mail].