How to load multiple dcd files for PCA?

[Cheng]

Dear Bio3D, I am following this link for the PCA.

I have 6 dcd trajectory files (2 mutants x 3 repeats). I would like to analyse PCA for all of them together, and plot them in different colours like the Figure 4 in the link does.

For example, 1) Use 6 different colours to represent different trajectories 2) Use 2 colours, each representing a mutant 3) Ideally, a drawing that can capture all the grouping information, e.g. squares and circles represent two mutants; three colours represent three repeats, with light to dark gradient represent PDB frames throughout the trajectories.

Can I ask how to achieve this?

Thank you.

Yours sincerely Cheng

[Barry Grant]

Can you not combine them like you can any two matrix objects?

[Cheng]

Hi @BarryG Sorry I am not sure what you were suggesting?

I got an answer about how to assign different colors and markers to differentiate the wild type from mutant, and repeats.

Now I am trying to combine 6 dcd files (2 mutants x 3 repeats) together, then run the PCA. However, because the two mutants have different atom numbers, I got error when combining them: Error: dcd file 4.dcd contains wrong number of atoms (6625).

Because the PCA only analyse the alpha-carbon atoms, so I think I only need the alpha-carbon entries in the dcd files. Based on the catdcd help:

should I make the protein.ind file like 5 16 25 37 if 5,16,25,37 are the atom indices for alpha-carbons?

Or, do you have other suggestions for analysing ensembles of 2 mutants * 3 repeats?