Calculate Phi, Psi angles

[Ashley Namini]

Hello, 

I am wanting to calculate the phi and psi angles for ensembles of Sic1. I am a bit confused on how the module works so I have a couple of questions. When I want to calculate phi angles, why can't MDAnalysis find atoms matching the names that it expects for residue 1? Likewise, when I want to calculate psi angles, why can''t MDAnalysis find atoms matching the names that it expects for residue 92? I am following the example from here:  https://userguide.mdanalysis.org/stable/examples/analysis/structure/dihedrals.html, "Selecting dihedral atom groups"

Thank you in advance for the help. 

Best, 

Ashley

[Hugo Macdermott-Opeskin]

Hi Ashley,

Welcome to the MDAnalysis mailing list! 

I am going to assume that Sic1 is the protein you are working on in your research.

Perhaps I can help you out a bit more if you share the  script you have written to analyse your dihedral angles and also the output that you would expect.

This snippet of code from the tutorial may help you identify if a residue has a non-standard name:

for res in u.residues:

    phi = res.phi_selection()

    if phi is None: 

        names = None

    else:

        names = phi.names

    print('{}: {} '.format(res.resname, names))

This will spit out each residue name and the selection used to define the phi angle allowing you to pinpoint residues with non-standard names etc.

Let me know how you go.

Cheers

Hugo

[Lily Wang]

Hi Ashley,

Does the protein end or have a break at residue 92? As phi is the C-N-CA-C angle and psi is the CA-C-N-CA angle, phi or psi angles will not be found or calculated for the first or last residues of a chain, respectively, because of the lack of a continuing backbone.

Cheers,

Lily

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