Output from pca analysis
Issue #869
resolved
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.
Comments (4)
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reporter -
Hi,
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.
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reporter Thank you so much for your prompt reply! I will try it!
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I found that I can only attach one file.
the code in pca.R is
The normal pdb file is look like