PCA by torsion angles of selected residues

Issue #508 new
skal24
created an issue

Hi,

I am looking to do a PC analysis for a trajectory based on the torsion angles of selected set of residues. For example, I want to see the major torsions sampled for a particular tyrosine residue of a homotetramer and cluster them. How can I make bio3d to do a PCA based on the torsion angles of selected residues?

I use the following to read my dcd and pdb file and fit them. I have done PCA on xyz, but not on torsions. Can somebody help me on how to proceed?

library(bio3d) dcdfile <- list.files("/path/", pattern=".dcd") pdbfile <- list.files("/path/", pattern=".pdb")

dcd <- read.dcd(dcdfile) pdb <- read.pdb(pdbfile) noh.inds<-atom.select(pdb, 'noh')

xyz<-fit.xyz(fixed=pdb$xyz[1,], mobile=dcd, fixed.inds=noh.inds$xyz, mobile.inds=noh.inds$xyz)

comment: select tyrosine from all four segids PROA, PROB, PROC, PROD

tyr.inds<-atom.select(pdb, resno=c(652)) tyr<-atom.select(pdb, resno=c(652), value=TRUE)

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