4 | :ref:`gmx do_dssp <gmx do_dssp>`, :ref:`gmx rama <gmx rama>`,
5 :ref:`gmx wheel <gmx wheel>`
6 | To analyze structural changes of a protein, you can calculate the
7 radius of gyration or the minimum residue distances over time (see
8 sec. :ref:`rg`), or calculate the RMSD (sec. :ref:`rmsd`).
10 You can also look at the changing of *secondary structure elements*
11 during your run. For this, you can use the program
12 :ref:`gmx do_dssp <gmx do_dssp>`, which is an interface for the
13 commercial program ``DSSP`` :ref:`176 <refKabsch83>`. For
14 further information, see the ``DSSP`` manual. A typical
15 output plot of :ref:`gmx do_dssp <gmx do_dssp>` is given in
16 :numref:`Fig. %s <fig-dssp>`.
20 .. figure:: plots/dssp.*
23 Analysis of the secondary structure elements of a peptide in time.
25 One other important analysis of proteins is the so-called *Ramachandran
26 plot*. This is the projection of the structure on the two dihedral
27 angles :math:`\phi` and :math:`\psi` of the protein backbone, see
28 :numref:`Fig. %s <fig-phipsi>`:
32 .. figure:: plots/phipsi.*
35 Definition of the dihedral angles :math:`\phi` and :math:`\psi` of
38 To evaluate this Ramachandran plot you can use the program
39 :ref:`gmx rama <gmx rama>`. A typical output
40 is given in :numref:`Fig. %s <fig-rama>`.
44 .. figure:: plots/rama.*
47 Ramachandran plot of a small protein.
49 When studying :math:`\alpha`-helices it is useful to have a *helical
50 wheel* projection of your peptide, to see whether a peptide is
51 amphipathic. This can be done using the :ref:`gmx wheel <gmx wheel>`
52 program. Two examples are plotted in
53 :numref:`Fig. %s <fig-hprwheel>`.
57 .. figure:: plots/hpr-wheel.*
60 Helical wheel projection of the N-terminal helix of HPr.