Hi Bianca, If the domains are rotated between the trajectories, the motion cannot be captured by a single linear component. Think of projecting an arc on a straight line. You loose the (deflection) part on the second component. That looks like squashing. I've mentioned this in relation to MD simulations in a paper about TRAIL and DR5.
Hope it helps, Tsjerk On Tue, Jan 14, 2014 at 3:48 AM, Bianca Ihrig <bian...@bii.a-star.edu.sg>wrote: > Hi everyone, > > I have been doing PCA using bio3d. My protein of interest has two domains > and there are two crystal structures, one in a closed (domains are close > together) and one in an open state (domains are nearly opposite each > other). I ran MD simulations on both states and did PCA. When doing PCA on > either of the trajectories it is working fine but when I combine the two > trajectories and all the frames to only one of the domains (as I would like > to see the motion of the other domain for closed vs. open state). > But when doing so the second domain (the one I am not align to) is > "squashed" when viewing the vectors in pymol. I dont understand why and I > dont know how to fix it. > Many thanks in advance for your time and help! > > This is the command I am using: > > R > library(bio3d) > > #read pdb file for open structure > pdbo <- read.pdb("ref-open(fr1800).pdb") > #to check: print(pdbo) > #read pdb file for closed structure > pdbc <- read.pdb("ref-closed(fr9990).pdb") > > #read traj files > tc <- read.ncdf("A2-closed-1001fr-100ns.nc") > to <- read.ncdf("A2-open-100ns-1000fr.nc") > > #combine the two traj (to and tc) into one called t2 > t2 <- rbind(tc[2:1001,],to[2:1001,]) # 2000 frames 10413 coordinates > > #Select residues of 1st domain (WHA) for alignment > whacac <- atom.select(pdbc, resno="9,10,11,12,13,14,15,16, > 17,18,19,20,21,22,23,24,25,26,27,47,48,49,50,51,52,53,54,56, > 55,57,58,59,60,61,62,63,64,66,67,68,69,70,78,79,80,81,82", elety = "CA") > #Select CA of the two pdb files > cao <- atom.select(pdbo, elety = "CA") # 215 atoms > cac <- atom.select(pdbc, elety = "CA") # 215 atoms > > # align the combined trajs to 1st domain of closed structure > xyz <- fit.xyz(fixed = pdbc$xyz, mobile = t2, fixed.inds = whacac$xyz, > mobile.inds = whacac$xyz) > #to check use command: write.ncdf() > > #####-- Do PCA over CA of the whole protein (not only domain 1) > pc <- pca.xyz(xyz[, cac$xyz]) > png("pca_open-closed.png") > pc1 <- plot(pc) > dev.off() > #view pc vector in pymol > view.modes(pc, mode = 1, outprefix = "pc1", scale = 30, dual = FALSE, > launch = TRUE) > > Many thanks! Your help is much appreciated! > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/ > posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > -- Tsjerk A. Wassenaar, Ph.D. [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.