bug using pdbaln

[Former user]

I use a Windows computer. When I try using the comand

pdbs <- pdbaln(c("4q21", "521p"), fit=TRUE, exefile="/path/muscle_v5.0.1428_windows.exe")

it gives me this error:

Error in file(file, "r") : cannot open the connection In addition: Warning messages: 1: In shell(paste(shQuote(exefile), cmd), ignore.stderr = !verbose, : '"/Users/Raquel/Downloads/muscle_v5.0.1428_windows.exe" -in C:\Users\Raquel\AppData\Local\Temp\RtmpkzG0YJ\file1538650819a6 -out aln.fa -seqtype protein' execution failed with error code 1 2: In file(file, "r") : cannot open file 'aln.fa': No such file or directory

How can I solve this error?

[Xinqiu Yao]

Hi,

‌

Bio3D does not support MUSCLE version 5 yet. Please install version 3 and try it again.

[cao jian]

I also meet this problem，I use ubuntu ,my code is

files <- get.pdb(c("4q21","5p21"), path=tempdir(), overwrite=TRUE)
pdbaln(files)

it give me this error:

Error in file(file, "r") : cannot open the connection In addition: Warning message:
In file(file, "r") : cannot open file 'aln.fa': No such file or directory

How can I solve this error ?

[Xinqiu Yao]

Which version of muscle and bio3d do you use?

[cao jian]

At first I use the MUSCLE version 5 and then I changed version 3.8 ,now it works, thank you very much!