Perl Or Python Script To Calculate Phi,Psi Angle Of A Pdb File

Question

[Siddharth]

Hi all...can anybody please give me perl or python script to calculate phi,psi angles from a pdb file? otherwise if u can provide a link which explains how to write such a script ? also any server which calculates phi,psi values will also be helpful....

[User 1933]

There is also an option to call R from Python/Perl, then you can get tremendous advantages of wide range of R package, Regarding your question you can look at Bio3d package

Answer 1

[Jeroen Van Goey]

From http://www2.warwick.ac.uk/fac/sci/moac/students/peter_cock/python/ramachandran/calculate/

The are at least three python libraries which can be used to load PDB files and calculate the protein backbone's φ/ψ angles:

• Konrad Hinsen's Molecular Modelling Toolkit (MMTK). Fussy about loading certain flawed PDB files, but getting phi and psi is very easy.

• Thomas Hamelryck's Bio.PDB module in BioPython. Tolerant of odd PDB files, making it a safer bet.

• Python Macromolecular Library (mmLib). Might be worth a look - but I haven't had time.

Provided your PDB files has nothing to funny in it, then I think using MMTK is the easiest way to get protein backbone deihedral angles in python. However, as Bio.PDB is much more tolerant of real world PDB files, it is a better choice for "data mining" tasks like calculating Ramachandran angles.

The page goes on to give code examples of the three options.

Answer 2

[Neilfws]

The WHAT IF server calculates torsion angles (click the Protein Analysis link) and a whole lot more.

[Siddharth]

Thanks to all for replying...I also got checked it with VADAR server...also with DSSP(dictionary of secondary stryucture of proteins)..

Answer 3

[nahsivar]

As mentioned above, many packages can do this job. (Biopython, Bioperl , Biojava, Bio3D, MMTK, Pymol, VMD, Chimera, YASARA, etc., ) and - the popular secondary structure calculation tools namely DSSP & Stride outputs phi/psi angles.

There is also a well established, fast code written in C, called torsions.c

Another good program called Dangle, a java-code also provides this along with the other torsion angles including side chain torsions (chi1, chi2, chi3 etc., ) - this is from Richardson's lab who has created MolProbity (that extensively checks the goodness of a protein structure based on allowed regions in Ramachandran space & clashes etc.,)

PRODY, a very good package developed in the past 2-3 years (since the previous posting & answers) also does this phi/psi calculation well.

Another tool, part of the pdb-tools package available on Google Code, also has a python script for this calculation!

Answer 4

[jamie.a]

I have written a python script to compute torsional angles which is shared on my GitHub here: https://github.com/jamie-alnasir/artemis/blob/master/Artemis.py

Alternatively, if you prefer a visual tool, my molecular viewer Zeus (for Windows) is able to load quite a few molecular file formats and compute torsional angles on PDB structures: http://www.al-nasir.com/portfolio/zeus/