NMA mktrj animated visualization PDB

[Daniel Lim]

Hello everyone, I was successfully able to run NMA on a single protein. However, as I came across the “mktrj()” function, I was not able to visualize my protein structure as a cartoon. Interestingly, the movement and the animation works without any problems. The only problem is that the outputted PDB was giving only ALA residues, so the outputted NMA trajectory PDB just looks like scattered points that are moving. I also ran the tutorial online step-by-step, copying and pasting the same code with the same protein (on the tutorial), and it also gave me only ALA residues (thinking there was a problem with my protein on my end). Is it only supposed to show the ALA residues by default? Is there a way I can show the animated NMA movement/fluctuations with my protein represented as a cartoon on PyMol? (I also thought PyMol was the issue, so I opened through VMD, and it still gave me the same result because the written PDB file only contained ALA residues).

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Please let me know if there is a way to visualize NMA on my protein as a cartoon model, rather than points.

Thank you in advance,

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Daniel

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[Barry Grant]

Pass the mktrj() function an appropriate pdb object with the residues you want. By default the write.pdb() function will use all ALA residue names and CA and atom type if you don't tell it otherwise.

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For viewing Calpha only models you should select a visualization style that shows Tube or Trace etc. All atom displays on Calpha only will just show isolated Calpha atoms in some viewers