rmsd average and pca frame extraction
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
Comments (6)
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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?
I am after an example, like you show in your tutorial.
Thank you
Loki
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Hi,
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 argumenta
; 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)
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.
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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?
Thank you again for helping.
Loki
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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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That is great, thank you very much for your kind help.
Loki
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