Reading PDB file from local disk

[Former user]

I try to read the file from a local disk: The commands given are:

library(bio3d) setwd("/home/prasanth/GNM/AURKA/GNM/Free/") pdb <- pdb.read("4j8n") pdb <- read.pdb("4j8n")

Warning message: In get.pdb(file, path = tempdir(), verbose = FALSE) : /tmp/RtmpzUUPyz/4j8n.pdb exists. Skipping download

I believe that this warning is due to the presence of a preexisted file. How can I read the file from a local disk without any error.

Please also note that command which incorporates system.file DOESNT work for me. pdb <- read.pdb( system.file("/home/prasanth/GNM/AURKA/GNM/Free/4j8n", package="bio3d") ) Error in read.pdb(system.file("/home/prasanth/GNM/AURKA/GNM/Free/4j8n", : No input PDB file found: check filename

[Xinqiu Yao]

Hi,

Yes, the warning just indicates that you have an existing pdb file, which you can safely ignore.

When reading from local disk, just provide the path and the full name of the pdb file. Note that in the above, you have missed the extension .pdb. Don't use system.file() - it is completely unrelated here.