How PCA contribution analysis reads residue numbers from PDB files instead of starting at 1

[dengwuji]

Hi , forgive my unfamiliarity with the R language, I'm doing PCA Contributions need to analyze how to read residue numbers from the PDB file instead of starting with 1.I am not familiar with the R language, can you please give an example or modification? Thank you very much! My original code:

library("bio3d")

dcd <- read.dcd("10_100_dt10.dcd")
pdb <- read.pdb("pro_ligand.pdb")

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)

png("ca-pca_contribution.png", width = 8, height = 4, units = "in", res = 1000)
par(cex.axis = 0.5)

plot.bio3d(pc$au[,1], ylab="Contribution", xlab="C-alpha Position", typ="l", xlim=c(1, length(pc$au[,1])), col="#FF9671")
points(pc$au[,2], typ="l", col="#0089BA")

x_ticks <- seq(25, length(pc$au[,1]), by=50)
x_labels <- seq(25, length(pc$au[,1]), by=50)

axis(side = 1, at = x_ticks, labels = FALSE, tcl = -0.2)
mtext(x_labels, side = 1, at = x_ticks, line = 1, cex = 0.5)

axis(side = 2, cex.axis = 0.5)

box()

legend("topright", legend=c("PC1", "PC2"), lty=c(1, 1), col=c("#FF9671", "#0089BA"))
dev.off()

[Xinqiu Yao]

If you simply want to label the plot with actual PDB residue numbers, try plot.bio3d(..., resno=pdb).

Hope it may help.

[高波]

Hello, yao.

forgive my unfamiliarity with the R language. if i want to generate the heatmap dccm with actual pdb residue number from x and y axis, how could i fix the code?

library(bio3d)
dcd <- read.dcd("D:/postdoc/MD/1pvh/analysis/traj/1pvh_bio3d.dcd")
pdb <- read.pdb("D:/postdoc/MD/1pvh/analysis/lif_topology-coot-0.pdb")
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])
plot(cij)

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i want to change the starting number iinto 34.

[Xinqiu Yao]

Hi,

‌

Try plot(cij, resno=pdb)

[高波]

Thanks Yao，for your kindly reply. if i want to show 3 differnt chains complex dccm, how could i change the x -axis and y-axis scale , to show chain a,b,c numbers（chain A:34-202; chain B: 124-320; chain C:246-396 ）? where could i search the tutorials, i have no idea after visiting your bio3D website?

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[高波]

i have visiting your bio3D website and the tutorials, but i couldn’t see the description for different chain' s dccm analysis. forgive my foolish, hoping for your kindly reply. thanks!

[Xinqiu Yao]

Hi,

‌

You will need to set the ticks and labels manually, which is a bit complicated. I would suggest to use the ‘margin.segments’ to indicate chains. For example,

plot.dccm(cij, resno=pdb, margin.segments=c(rep(1,XX), rep(2, YY), rep(3, ZZ)))

Replace XX, YY, and ZZ with the length (number of residues) of chain A, B, and C, respectively.

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If you really want to change the scale, try the following:

ca.inds <- atom.select(pdb, "calpha")
resno <- pdb$atom$resno[ca.inds$atom]
chain <- pdb$atom$chain[ca.inds$atom]
xy.at <- pretty(1:ncol(cij))
xy.at <- xy.at[xy.at <= ncol(cij)]
xy.at[1] <- 1
labs <- paste(chain[xy.at], resno[xy.at], sep=":")
scales <- list(at=xy.at, labels=labs)
plot.dccm(cij, scales=scales)

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[高波]

Thanks for your kindly and generous reply. Hope you having a nice day!