Can it creat a ramachandran plots from pdb?

[city10th]

Hi. It's a great project. I am new here. I notice that there is no pdb file in your example. So, I want to know whether it can creat a ramachandran plots from pdb. If it can, please give a example.

[KarlTDebiec]

Hi @city10th,

Unfortunately Ramaplot does not currently support this conveniently. I typically use it such that each plot corresponds to a single amino acid, for example the Φ/Ψ sampling of each residue over the course of a molecular dynamics simulation trajectory. Ramaplot doesn't currently have any functionality to calculate Φ/Ψ from a structure; it exclusively reads in Φ/Ψ values that have been previously calculated using another program. This is a feature I may implement in the future.

My recommendation is to use the program Visual Molecular Dynamics. VMD can load the PDB, and the Ramachandran plot plugin (accessible from Extensions > Analysis > Ramachandran Plot) gives a nice interface for looking at the overall Φ/Ψ of a single structure from a PDB.

Best,
Karl