Hello, I have been trying to use MUSTANG for structure base alignment instead of sequence based alignment. However, I have been getting issues. I have checked the bio3d index of the mustang commands to use, but they're not getting the job done. I want to clarify if this is a Bio3D problem or not. The screenshots show that MUSTANG is working fine, but they're are errors that I do not know of. Please let me know if you have any insights to this. Thank you in advance!

What I have in my script:

Setting working directory

setwd("~/Dropbox/712_homologPDBs/loops_refines/mehmet_nmaI/minimized_V1")

Using package

library(bio3d) library(parallel)

Storing all minimized PDBs into single list

Extracting list from renamed PDBs

pdbfiles <- list.files('fitted/', pattern = ".pdb", full.names = TRUE)

Beginning Sequence Alignment

Multiple Sequence Alignment

Extract and align sequences

pdbs <- mustang(pdbfiles, exefile='/usr/local/bin/mustang-3.2.3')

Fetching IDs

pdbs$id <- substr(basename(pdbs$id), 1, 4)

Storing in "ids"

ids <- pdbs$id

Calculating Sequence Identity

Not really relevant, but we can show the rationale behind why we are using structural based alignment instead

seqidentity(pdbs)

Calculating RMSD (xyz differences)

Lower #, the better

Fit = TRUE to reduce RMSD values

rmsd(pdbs, fit = FALSE)

Getting error like this after i try to run rmsd(pdbs): “Error in matrix(colSums(rbind(gap.pos1, gap.pos2), na.rm = TRUE), ncol = ncol(x)) : non-numeric matrix extent”

Using MUSTANG for structural alignment