Error in dssp.pdb(pdb) - unhelpful error message

[Former user]

Running the following code, I get the error message below:

pdb = read.cif("https://files.rcsb.org/download/5aj0.cif") pdb = trim.pdb(pdb, inds = atom.select(pdb, chain = "AA")) pdb = clean.pdb(pdb, force.renumber = TRUE, rm.lig = TRUE, fix.aa = TRUE, rm.wat = TRUE) dssp(pdb)

Error in dssp.pdb(pdb) : An error occurred while running command 'mkdssp /var/folders/2d/qxrc40l12zxf5bmhcz2tm4ch0000gn/T//RtmpPgT5vk/file5ce538f71ee1 /var/folders/2d/qxrc40l12zxf5bmhcz2tm4ch0000gn/T//RtmpPgT5vk/file5ce5680c62fe'

I've run dssp successfully with other pdbs and cifs, so I'm not sure why this one fails and the error message does not give me any clues. Any ideas on how to troubleshoot?

Thank you

[Xinqiu Yao]

Hi,

Most likely it is because dssp doesn't recognize chain ID with two letters. Try

pdb$atom$chain <- 'A'
dssp(pdb)

It should work.

[Xinqiu Yao]

Question not a bug

[Xinqiu Yao]

No response from the user.