Hello!

I have downloaded the BiocManager "muscle" package, but when I try to use functions that would use the package, it says muscle is not installed/working properly. I was wondering if anyone could help me or direct me to a resource where I could find help.

Thank you, Carleigh Oberkfell

Here is the error message I get after using the command:

> pdbs<-pdbaln(files)
Reading PDB files:
split_chain/1g7a_A.pdb
split_chain/1g7a_B.pdb
split_chain/1g7a_C.pdb
split_chain/1g7a_D.pdb
split_chain/1g7a_E.pdb
split_chain/1g7a_F.pdb
split_chain/1g7a_G.pdb
split_chain/1g7a_H.pdb
split_chain/1g7b_A.pdb
split_chain/1g7b_B.pdb
split_chain/1g7b_C.pdb
split_chain/1g7b_D.pdb
split_chain/1g7b_E.pdb
split_chain/1g7b_F.pdb
split_chain/1g7b_G.pdb
split_chain/1g7b_H.pdb
split_chain/2wrx_A.pdb
split_chain/2wrx_B.pdb
split_chain/2wrx_C.pdb
split_chain/2wrx_D.pdb
Extracting sequences
Error in seqaln(s, id = files, ...) : 
  You do not have muscle installed/working locally on your machine.
  We can attempt to use the EBI webserver if you provide an email address (required by the EBI).
  Please note that the EBI states (see their Terms of Use):
     'Using fake e-mail address may result in your jobs being killed and your IP, Organisation or entire domain being black-listed.'

Here is my session info:

> sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] muscle_3.28.0       Biostrings_2.54.0   XVector_0.26.0      IRanges_2.20.2      S4Vectors_0.24.3   
[6] BiocGenerics_0.32.0 devtools_2.2.1      usethis_1.5.1       bio3d_2.4-1.9000   

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.3          magrittr_1.5        zlibbioc_1.32.0     pkgload_1.0.2       R6_2.4.1           
 [6] rlang_0.4.4         fansi_0.4.1         tools_3.6.2         pkgbuild_1.0.6      grid_3.6.2         
[11] sessioninfo_1.1.1   cli_2.0.2           withr_2.1.2         remotes_2.1.1       ellipsis_0.3.0     
[16] assertthat_0.2.1    digest_0.6.23       rprojroot_1.3-2     crayon_1.3.4        processx_3.4.1     
[21] BiocManager_1.30.10 callr_3.4.2         fs_1.3.1            ps_1.3.0            testthat_2.3.1     
[26] memoise_1.1.0       glue_1.3.1          compiler_3.6.2      desc_1.2.0          backports_1.1.5    
[31] prettyunits_1.1.1

The function in question is from the package bio3d which is a CRAN package. Unfortunately there is a miscommunication here as it seems like there is a R package called muscle that is in Bioconductor as well as a system requirement muscle that needs to be installed on your computer and in your paths. The muscle that bio3d is referring to is not the Bioconductor package. You should check the http://thegrantlab.org/bio3d/tutorials/installing-bio3d instructions specifically the section for MUSCLE