I need to download multiple PDB files (more than 300 pdb files) from PDB data bank and to read Ramachandran angles of specific residues in each PDB file. How could I do that in python? If not in python , is there any other software or anything to do the same?
Use biopython. The Bio.PDB.internal_coords module contains the classes to support internal coordinates for protein structures.
https://biopython.org/docs/dev/api/Bio.PDB.internal_coords.html
"Internal coordinates comprise Psi, Phi and Omega dihedral angles along the protein backbone, Chi angles along the sidechains, and all 3-atom angles and bond lengths comprising a protein chain. These routines can compute internal coordinates from atom XYZ coordinates, and compute atom XYZ coordinates from internal coordinates."
Dear Vigneshwaran Kannan
Have a look: https://www.mathworks.com/help/bioinfo/ref/ramachandran.html
Kind Regards
Qamar Ul Islam
Use rama2img.py script (open eye) as follows:
Just put them in a loop to do it iteratively.
wget https://files.rcsb.org/download/2rox.pdb
python3 rama2img.py -in 2rox.pdb -out 2rox.svg
Thanks everyone Ramin Ekhteiari Salmas Qamar Ul Islam Annemarie Honegger I ll try everything
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