GeoStaS analysis in differentiate mode

[Mahnaz Tehrani]

Hi all,

I would like to do GeoStaS analysis in differentiate mode to find differences between protein domains in different states of a target protein. So I have an ensemble of PDB files for each state (1000 frames) as follows:

# Load libraries

library(bio3d.geostas, lib.loc = "/home/zahra/R/x86_64-suse-linux-gnu-library/4.0")

library(bio3d.core, lib.loc = "/home/zahra/R/x86_64-suse-linux-gnu-library/4.0")

# Read PDB files

pdb1 <- read.pdb("state1.pdb", multi = TRUE)

pdb2 <- read.pdb("state2.pdb", multi = TRUE)

pdb3 <- read.pdb("state3.pdb", multi = TRUE)

# Perform geometric statistics analysis with k=6 for all datasets

gs1 <- geostas(pdb1, fit = TRUE, k = 6)

gs2 <- geostas(pdb2, fit = TRUE, k = 6)

gs3 <- geostas(pdb3, fit = TRUE, k = 6)

# Calculate differentiated geostatistical matrices

diff_gs_s1_s2 <- gs1$amsm - gs2$amsm

dim(diff_gs_s1_s2)

diff_gs_s3_s1 <- gs3$amsm - gs1$amsm

dim(diff_gs_s3_s1)

diff_gs_s3_s2 <- gs3$amsm  - gs2$amsm

dim(diff_gs_s3_s2)

plot(diff_gs_s1_s2 contour=TRUE, main="Diff geostas-s1 vs geostas-s2”)

plot(diff_gs_s3_s1, contour=TRUE, main="Diff geostas-s3 vs geostas-s1")

plot(diff_gs_s3_s2, contour=TRUE, main="Diff geostas-s3 vs geostas-s2")

it worked fine all the way till plotting and plots are not resemble as plot(gs) in absolute mode annotated with protein residues. So I need to change plot command line to reproduce standard “Atomic movement similarity matrix with domain annotation”, given here:

Enhanced Normal Modes Analysis with Bio3D • Bio3D (thegrantlab.org)

I'd be grateful for any guidance/suggestions regarding my question.

Bests

Zahra