4.3 years ago by
This error message means that R cannot open a file. The question is, which file?
In my case, running bio3d on Ubuntu, I saw the same error message plus something extra:
In addition: Warning message:
In file(con, "r") :
cannot open file '/tmp/RtmphuZYHy/file1e5e7dbf452f': No such file or directory
Looking in /tmp/RtmphuZYHy there was indeed no such file, but there were other files with similar names which seemed to be derived from PDB files.
The mystery was solved by examining the code for the dssp() function, which you can do simply by typing "dssp". The first few lines:
function (pdb, exepath = "", resno = TRUE)
infile <- tempfile()
outfile <- tempfile()
write.pdb(pdb, file = infile)
system(paste(exepath, "dssp -c ", infile, " ", outfile, sep = ""),
ignore.stderr = TRUE)
The version of DSSP on my machine does not have the "-c" switch (which used to mean "create output in pre-1995 format"). Trying to run it outside of R with that switch gives an error. I will bet that your version of DSSP has the same issue.
So in summary: the dssp() function calls DSSP incorrectly (with an obsolete switch), therefore no output file is written, hence the error message.
To fix this, you will have to edit the code for that function. I'd also suggest filing a bug report with the authors of bio3d, if there is not one already.