Unable to launch Muscle package from pdbaln() function.

[Former user]

Following the tutorial on Normal Mode Analysis 1, I want to align pdb structures using the pdbaln function:

pdbs.all <- pdbaln(files, fit=TRUE)

Error in seqaln(s, id = files, ...) : Launching external program failed
  make sure 'muscle' is in your search path

#Library paths:
> .libPaths()
[1] "/Users/Jamie/R_packages/muscle/R"                              
[2] "/Library/Frameworks/R.framework/Versions/3.1/Resources/library"

I initially installed muscle in the default directory, then tried installing it locally with the same result. Could anyone please advise me on how to resolve this issue?

n.b. R 3.1.1, bio3d 2.1 Cheers, Jamie

---

Jamie Macpherson PhD Student, King's College London

[Lars Skjærven]

Hi Jamie, You can try to explicitly supply the path to the muscle exectuable (see help(seqaln) for details):

pdbaln(files, exefile="/usr/local/bin/muscle")

(assuming muscle is installed under "/usr/local/bin/muscle")

To avoid providing the path every time you should include "/usr/local/bin" (or your equivalent) to your search path. e.g. add the following line to your .bashrc file:

export PATH=/usr/local/bin:$PATH

[Jamie Mac]

Hi Lars,

Thanks for your quick response. I have tried defining the path to the muscle execution file:

pdbs.all <- pdbaln(files, exefiles="/Library/Frameworks/R.frameworks/Versions/3.1/Resources/library/muscle/R/muscle")

Unfortunately I still get the same error: Error in seqaln(s, id = files, ...) : Launching external program failed make sure 'muscle' is in your search path

Am I defining the wrong executable file? Is there are way around this?

Thanks, Jamie

[Lars Skjærven]

Could you try upgrading to version 2.2 of Bio3d? It's on CRAN, so

install.packages("bio3d")

would upgrade your bio3d installation.

[Lars Skjærven]

oh, and make sure it's exefile, not exefiles

[Jamie Mac]

Yes I am using Bio3d 2.2 and sorry I meant exe file (typo). Do I perhaps have to define the executable file within searchpaths() ?

[Lars Skjærven]

what happens if you do:

> system("/usr/local/bin/muscle -version")
MUSCLE v3.8.31 by Robert C. Edgar

[Jamie Mac]

system("/home2/jamesm/R/x86_64-redhat-linux-gnu-library/3.1/muscle/R/muscle -version") /home2/jamesm/R/x86_64-redhat-linux-gnu-library/3.1/muscle/R/muscle: line 19: syntax error near unexpected token {' /home2/jamesm/R/x86_64-redhat-linux-gnu-library/3.1/muscle/R/muscle: line 19:local({'

[Lars Skjærven]

This doesn't look right. why is there a syntax error? Try calling system("ls")

[Jamie Mac]

system("ls") Headers Libraries PrivateHeaders R Resources Versions raw_pdbs seqs.fasta temp.rafa

[Lars Skjærven]

Great. seems to be working. So why is there a syntax error two replies up? That's where you should focus. Which permissions are given to muscle? did you check that it runs from terminal?

[Barry Grant]

Hi Jamie, Looks like muscle is possibly not setup properly on your mac, can you reproduce what I see in my mac terminal:

barry$ which muscle
/Users/barry/bin/muscle

barry$ muscle
MUSCLE v3.8.31 by Robert C. Edgar
...<cut>...

To get this I renamed the muscle excitable to be just 'muscle' and moved it to be in my local ~/bin/ directory that is in my PATH environment variable, which in my case is define in a file called ~/.profile (although ~/.bashrc as Lars mentions above is also good). Here is the relevant line in my ~/.profile file.

export PATH=/usr/local/mysql/bin:~/bin:$PATH

[Jamie Mac]

Thank you both for your help. I made the silly mistake of trying to source the muscle R package binary instead of the standalone muscle program binary. After following your instructions it now works fine.

Thanks again for your help, Jamie

[Lars Skjærven]

Good!