pdbaln function

[Former user]

Hi everyone,

I was using pdbaln function to align the structures in bio3d. I have installed muscle in the working directory of R on windows. But it looks likes that it doesn't recognize muscle. So, please let me know how to resolve this issue.

[Lars Skjærven]

Hey, Argument exefile lets you specify the path where you have muscle installed. See also the documentation for more info.

library(bio3d)
seqs <- get.seq(c("4q21_A", "1ftn_A"))
aln <- seqaln(seqs, exefile="c:\Programs\muscle.exe")

Note that you can also use clustalo if you use the development version of bio3d.

[Barry Grant]

Lars's answer is a good one. Essentially, MUSCLE must be installed on your system and be in the search path for executables otherwise you will need the exefile argument to point to muscle directly. I am not a windows user but I believe you can you use 'System' from the Control Panel, selecting the 'Advanced' tab, the 'Environment Variables' button and then finding the PATH (user or system) and editing it accordingly. Thanks!