mustang(files, exefile="mustang", outfile="aln.mustang.fa", cleanpdb=FALSE, cleandir="mustangpdbs", verbose=TRUE)
Create a multiple sequence alignment from a bunch of PDB files.
Structure-based sequence alignment with MUSTANG attempts to arrange and align the sequences of proteins based on their 3D structure.
This function calls the MUSTANG program, to perform a multiple structure alignment, which MUST BE INSTALLED on your system and in the search path for executables.
Note that non-standard residues are mapped to Z in MUSTANG. As a workaround the bio3d mustang function will attempt to map any non-standard residues to standard residues (e.g. SEP->SER, etc). To avoid this behaviour use cleanpdb=FALSE.
Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.
MUSTANG is the work of Konagurthu et al: Konagurthu, A.S. et al. (2006) Proteins 64(3):559--74.
More details of the MUSTANG algorithm, along with download and installation instructions can be obtained from: http://www.csse.monash.edu.au/~karun/Site/mustang.html.
A system call is made to the MUSTANG program, which must be installed on your system and in the search path for executables.
## Fetch PDB files and split to chain A only PDB files ids <- c("1a70_A", "1czp_A", "1frd_A") files <- get.pdb(ids, split = TRUE, path = tempdir())|======================================================================| 100%##-- Or, read a folder/directory of existing PDB files #pdb.path <- "my_dir_of_pdbs" #files <- list.files(path=pdb.path , # pattern=".pdb", # full.names=TRUE) ##-- Align these PDB sequences aln <- mustang(files)Running command mustang -f /tmp/RtmpTDihxb/filecfdb57737ba6 -o /tmp/RtmpTDihxb/filecfdb453ee916 -F fasta##-- Read Aligned PDBs storing coordinate data pdbs <- read.fasta.pdb(aln)pdb/seq: 1 name: /tmp/RtmpTDihxb/split_chain/1a70_A.pdb pdb/seq: 2 name: /tmp/RtmpTDihxb/split_chain/1czp_A.pdb PDB has ALT records, taking A only, rm.alt=TRUE pdb/seq: 3 name: /tmp/RtmpTDihxb/split_chain/1frd_A.pdb