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GeoStaS analysis in differentiate mode
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
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