--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rmsf.R	Wed Mar 27 15:16:19 2019 -0400
@@ -0,0 +1,57 @@
+#!/usr/bin/env Rscript
+
+options(stringAsfactors = FALSE)
+args <- commandArgs(trailingOnly = TRUE)
+
+library(bio3d)
+
+dcdfile <- args[1]
+pdbfile <- args[2]
+selection <- args[3]
+
+dcd <- read.dcd(dcdfile)
+pdb <- read.pdb(pdbfile)
+
+
+if (selection == "string") {
+    domain <- args[4]
+    output <- args[5]
+    rmsf_plot <- args[6]
+    inds <- atom.select(pdb, string = domain)
+} 
+if (selection == "resno") {
+    res1 <- args[4]
+    res2 <- args[5]
+    output <- args[6]
+    rmsf_plot <- args[7]
+    inds <- atom.select(pdb, resno=res1:res2)
+} 
+if (selection == "elety") {
+    domain <- args[4]
+    output <- args[5]
+    rmsf_plot <- args[6]
+    inds <- atom.select(pdb, elety = domain)
+}
+if (selection == "resid") {
+    domain <- args[4]
+    output <- args[5]
+    rmsf_plot <- args[6]
+    inds <- atom.select(pdb, resid = domain)
+}
+if (selection == "segid") {
+    domain <- args[4]
+    output <- args[5]
+    rmsf_plot <- args[6]
+    inds <- atom.select(pdb, segid = domain)
+}
+
+xyz <- fit.xyz(fixed=pdb$xyz, mobile=dcd, fixed.inds=inds$xyz, mobile.inds=inds$xyz)
+
+rf <- rmsf(xyz[,inds$xyz])
+
+write.table(rf, file = output, row.names = TRUE, col.names = FALSE, quote =FALSE, sep="\t")
+
+png(rmsf_plot)
+plot(rf, ylab="RMSF", xlab="Residue Position", typ="l")
+dev.off()
+