rmsd average and pca frame extraction

[Former user]

Hi,

I am having trouble to run the rmsd command against an average structure. I also want to extract trajectories frames from the PCA graph but cannot figure out how to do that.

Can anyone help?

Thank you Loki

[Xinqiu Yao]

Can you describe your questions in more detail? An instruction is given in the IMPORTANT NOTES after you click Create issue.

[Loki]

Hi,

Well I dont know how to do it. I am following your tutorial but I have no idea how to create a graph of rmsd values against an average structure as opposed to the first structure as you show in your tutorial.

For the PCA, you say in the tutorial : How do you think you can extract the frame?

Well I dont know. How can you?

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I am after an example, like you show in your tutorial.

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Thank you

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Loki

[Xinqiu Yao]

Hi,

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For your first question, you can calculate the average structure from a fitted trajectory easily. Then, use the structure as the reference in rmsd() (put the structure as the value of the argument a; see ?rmsd for more detail). For example,

# Suppose you have read a trajectory and name it traj in R.
# If the trajectory is not fitted, you need to do the following step first.
xyz <- fit.xyz(traj[1, ], traj) 

# Calculate the average structure.
avg <- colMeans(xyz)

# Calculate RMSD against the average.
rmsd(avg, xyz, fit=TRUE)

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For the second question. Can you tell what specific tutorial you were looking at? I’ve gone through the website and couldn’t find the line you mentioned.

[Loki]

Hi,

Thank you so much for helping with this. Its truly appreciated.

The PCA analysis is in the begin trajectory analysis, specifically here: How can we find out which frames correspond to the distinct groups along PC1? HINT: Which variable/object created above tells us about cluster membership?

I wonder how can I extract the frames?

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Thank you again for helping.

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Loki

[Xinqiu Yao]

Well, for that particular question, the answer is grps, which contains the cluster membership ID for each frame of the trajectory. For example, grps[1] will be the cluster ID of frame No. 1, etc.

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[Loki]

That is great, thank you very much for your kind help.

Loki