PCA analysis (genration of blue red and white colored residues motion in pdb file)

[Armi Chaudhary]

hello team,

I had followed the trajectory analysis within BIO3D and successfully finished it for my trajectory.

While performing pca with following commands. i am getting the attached graph. and when I visualize the pdb file generated from mktrj function it shows all residues in while color. where in tutorial there is BLUE RED and white color is shown for HIV protease(hicpc1.png) . in plotted graph there is all blue white and red points then in pdb why it is only in white?

how to generate that different color motion graph.

pc <- pca.xyz(xyz[,casc.local.inds$xyz])
plot(pc, col=bwr.colors(nrow(xyz)) )

p1 <- mktrj.pca(pc, pc=1, b=pc$au[,1], file="pc1.pdb")
p2 <- mktrj.pca(pc, pc=2, b=pc$au[,2], file="pc2.pdb")

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[Armi Chaudhary]

MY PCA1 pdb in only white color.

[Armi Chaudhary]

i think this image can be taken through ncdf file. but in Linux ubuntu this package is not installing please guide me with this?

[Xinqiu Yao]

Hi,

‌

The PCA results you showed look weird. Did you fit structures properly? You might want to fix this issue first before moving on.

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The hivp figure was generated with VMD. You can find more detail about how to use the software from their website:

https://www.ks.uiuc.edu/Research/vmd

[Armi Chaudhary]

blacked colored image in where colored loop structure is shown that image i tool in discovery studio. and I fit structure with fit xyz command.

[Barry Grant]

Agree that something looks off in your analysis that you want to check first. However, to color like the second figure you will want to just select “color by B-factor” in VMD or whatever viewer you are using as that that is where you have mapped the residue wise loadings (i.e. how much each residue contributes to the PC).

Good luck!