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Generating Cartesian coordinates of each atom in protein chain from the internal coordinates using python or some software

Biology Asked by vigneshwaran kannan on December 2, 2020

I am trying to compute Cartesian coordinates of backbone atoms and side-chain atoms (C beta alone) for a given set of internal coordinates (bond lengths, bond angles and dihedral angles) I have written a code for the backbone alone (i.e) to construct cartesian coordinates of each atom in backbone from the respective internal coordinates(without side chains). However I got to know that this can be done in a software (maybe in PyMol or VMD). I am completely a beginner in this field of biochemistry/bioinformatics/biophysics. Does it really possible to do this in software like PYMOL/VMD? I’ll be very happy if I can do this in python itself. I want to generate cartesian coordinate of a given tetrapeptide for all possible Ramachandran angles (within the allowed region)

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