POLYVIEW-3D Tutorial
Part 2. Overall structure view
Structure models
When the file contains multiple structural models (e.g., molecular
structures derived using NMR, or alternative docking
models of protein complexes), one can specify the model to
be rendered (by entering its number). However, this setting
is discarded when the option
Animate models from
Animation settings is chosen.
If the number of the model is not specified, then the
first model is used for rendering.
Top two panels below illustrate how to select a specific
model (by entering its
number) from an NMR ensemble of structures, using as an
example a scorpion peptide/toxin (PDB id
1acw). Second row of panels below shows an
example of toggling between
asymmetric and
biological units, using
the structure of a porin from Rh. blastica
(PDB id 1bh3).
| Render model 1 (Default option) |
Render model 11 |
|---|---|
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|
Ligand and solvent data
Ligands (chemical moieties defined in HETATM sections
within PDB files) and solvent (e.g., water) molecules can
be optionally rendered along with the macromolecular
structure. By default, ligands are shown as spheres, but
can also be rendered as sticks. Water molecules are always
shown as balls. In both cases, small molecules are colored
using the CPK color scheme (by atom types).
Example below represents crystal structure of the Phot-LOV1 domain from Chlamydomonas reinhardtii in the dark state (PDB id 1n9l), with sulfate anion and flavin mononucleotide ligands shown using sphere and stick models, respectively.
| Render ligands as spheres (Default option) |
Render ligands as sticks |
|---|---|
|
|
| Show ligands and water | Hide ligands and water |
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| Click on respective image to see options used for its rendering. | |
Initial orientation
There are several options to change the default projection of the structure, which is defined in the PDB file. One possibility is to specify explicitly the rotation angles (in degrees) around the three main axes (X, Y, Z). These rotations are applied to the original orientation in the order of appearance. However, the trial and error process of setting these angles manually can be tedious. To simplify it, one can use the Java-based Jmol viewer in order to select interactively the desired projection and rotation angles that are subsequently passed to the main submission form.
In many instances, it is important to highlight some particular structural elements, e.g., a mutated amino acid residue or a ligand binding pocket. However, the point of special interest typically does not correspond to the center of rendered image. In POLYVIEW-3D, one can optionally specify the center of view by entering the residue number and/or chain label. If the chain label is given without specifying a residue of interest, the chain centroid will be placed at the center of the view. Alternatively, just like the orientation, the center of focus can be specified using Jmol: clicking on residue of interest within the interactive Jmol window to assign it as a center of view will do the trick. Centering view can be also coupled with zooming.
Example below shows how the initial orientation of a protein structure can be adjusted to make its ligand binding pocket more visible. Centering and zooming options are also used in this case to highlight the ligand binding pocket better. Here, interior cavity of T4 lysozyme (PDB id 182l) is shown with two ligand specific pockets that distinguish more rigid chemical structures (benzofuran, in this case, located deeper in the cavity) and more flexible ones (2-hydroxyethyl disulfide, located in outer pocket).
| Render protein and ligands (Default option) |
Orient and center structure | Zoom in the pocket |
|---|---|---|
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| Click on respective image to see options used for its rendering. | ||