Hello everybody, Iam Ram kumar. May i know how to calculate phi and psi angles with x,y,z co-ordinates from PDB files.. is there any formula to do ..?

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[John D'Errico]

Of course there is a formula. What you mean by phi and psi angles, we don't know. Maybe it has something to do with spherical coordinates. If that is it, then why would you not just use google instead of waiting for a response?

https://en.wikipedia.org/wiki/Spherical_coordinate_system

That your numbers come from whatever file type you have, you need to learn to read the numbers into MATLAB. That has nothing at all to do with any formula anyway.

[Ram kumar Masilamani]

john, phi and psi are dihedral angles of amino acid residues present in protein. I need to calculate phi and psi angles of each and every residue. u have suggest me spherical coordinate system. with my knowledge it is different from torsional angles. thank u for your suggestion.

Answer 1

[Luuk van Oosten]

Dear Ram Kumar,

You could use Ramachandran. If you do something like the following:

Kumar = ramachandran('Your_PDB_database_identifier')

You will have the 1x1 struct 'Kumar' in your workspace. Access the angles (phi, psi and omega) by:

Kumar.Angles

You could also do it as D'Errico described. In that case you could just open a *.PDB file as follows:

Kumar_pdbstruct = pdbread('your_pdb_file_name.pdb');

And then access the XYZ coordinates using

Kumar_pdbstruct.Model.Atom

There you will have the XYZ coordinates of every atom in the protein model, and you can calculate the corresponding dihedral angles yourself.

Have fun.

[Ram kumar Masilamani]

hello oosten, thank u so much. From your suggestion I have found the X,Y,Z coordinates of each and every residue. But I have to calculate these angles by using formulas. I have used number of formulas in matlab, but I couldn't work out those. will u please tell me a formula .?

[Luuk van Oosten]

I recommend you have a look at this article. It has a very detailed explanation of all the formulas and calculations to get the angles from XYZ coordinates.

[Walter Roberson]

Luuk van Oosten: it appears to me that article is about calculating XYZ coordinates from angles; at least the abstract only mentions that direction.

[Luuk van Oosten]

That is correct. Nevertheless, it would be a good starting point, as the article also refers to other work which describes different algorithms. Another quick google search also gives you this small, but nice explanation, which would be another place to start calculating the angles from Cartesian coordinates.