Output from pca analysis

[Liu Qianchen]

Hello,

There are some unusual bonds in “pc1.pdb” file between the end of the peptide and the protein, and between the two peptides. I am not sure whether I did it wrongly, and I attached the input file “pca.R“, “pc1.pdb”, and the normal pdb file.

Thank you for your time and help.

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[Liu Qianchen]

I found that I can only attach one file.

the code in pca.R is

The normal pdb file is look like

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[Xinqiu Yao]

Hi,

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I think it is the VMD visualization problem. Somehow VMD doesn’t honor TER or even chain IDs if only CA atoms are present. The trick is to renumber residues from 1 for each chain. For example,

pdb <- read.pdb("pc1.pdb", multi=TRUE)
pdb$atom$chain[1:185] <- 'A'
pdb$atom$chain[186:206] <- 'B'
pdb$atom$chain[207:227] <- 'C'
pdb$atom$chain[228:248] <- 'D'
pdb <- convert.pdb(pdb, renumber=TRUE, consecutive=FALSE)
write.pdb(pdb, file="pc1-fixed.pdb") 

This should work.

[Liu Qianchen]

Thank you so much for your prompt reply! I will try it!