error using pdbaln()

[Former user]

pdbs <- pdbaln(files,fit=TRUE,exefile="~bin/muscle")

Error in matrix(unlist(retval[, "res.ss"]), nrow = length(aln$id), byrow = TRUE) : 'data' must be of a vector type, was 'NULL' In addition: There were 50 or more warnings (use warnings() to see the first 50)

Warning messages: 1: In pdb2sse(pdb) : No helix and sheet defined in input 'sse' PDB object: try using dssp() 2: In pdb2sse(pdb) : No helix and sheet defined in input 'sse' PDB object: try using dssp() 3: In pdb2sse(pdb) : No helix and sheet defined in input 'sse' PDB object: try using dssp() 4: In pdb2sse(pdb) :

[Lars Skjærven]

Hi, Can you provide some more information, e.g. what is the content of files, which bio3d version are you using, and if the separate files are readable? can you do

for(f in files) 
    read.pdb(f)

[Xinqiu Yao]

Hi, try what Lars suggested and also try to check if the spell was correct: "~bin/muscle" (Usually should be "~/bin/muscle").

About warnings, we probably should mute it by default, since in most cases we don't have SSE records in pdb files (e.g. after calling pdbsplit()).

[Lars Skjærven]

reopen if needed