I've been reading on Protein Amino Acid Sequences and their 3D structure. It seems that the 3D structure is encoded by the three torsion angles as shown above. My professor said there is a 1-1 encoding between 3d cartesian coordinates and the torsion angles, but I cannot find any way to do this either in pyrosetta or biopython. Is there any formulas/packages that would be of use for this conversion?

  • $\begingroup$ Do you want to calculate the dihedrals from the coordinates? That's easy enough - use something like dang kinemage.biochem.duke.edu/software/dang.php. For the other way round, see rosettacommons.org/content/… $\endgroup$ – gilleain Feb 13 at 8:55
  • $\begingroup$ Welcome to SE Biology. If your professor said really said that (and I imagine he qualified it in some way), he should be fired; and you should reconsider whether angles alone can determine (not encode) a structure in which there are different amino acid residues with bonds of various length. Do you actually have any imput data for the program you can't find? You should ask yourself what is the experimental data in the real world that would need computer processing. Are there experimental techniques for determining dihedral angles, or are they deduced from the determined 3D co-ordinates? $\endgroup$ – David Feb 13 at 9:04

As I indicated in my comment:

  1. You need the amino acid sequence and values for bond lengths before you could determine the atomic co-ordinates from the dihedral angles.
  2. Originally the dihedral angles are calculated from the experimentally atomic co-ordinates (with the help of the sequence), so that what you propose is in its nature an academic exercise.

There is, however, a situation in which I have — in effect — done that, in exploring the structures that would be produced if the dihedral angles were varied. Rather than a command-line tool, there is a graphical tool that allows you to vary the angles interactively and see the results. This is the excellent Ramachandran Plot Explorer (Rama) by Bosco Ho. And yes, it can also generate the co-ordinates — you can save the results in PDB format to reopen or to visualize with other protein graphic software, such as JSmol.

The only problem is that the last version of this software was released in 2006, and is not 64-bit, so it will not run on the next version of Mac OS X (no idea about Windows). Bosco’s blog is still active, so perhaps he could be persuaded…


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