cuemol2/Prot2ndryStr

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Protein secondary structure assignment

The ribbon and cartoon renderers in CueMol display the protein main chain structures based on their secondary structure, i.e., helix, strand, and coil. This section explains how to assign the protein secondary structure to the molecular (MolCoord) objects.

Assignment when opening the PDB file

The protein secondary structure is automatically assigned to the molecule, upon the opening of the PDB (and mmCIF, etc.) file. You can choose the method of the assignment in the “File open options” dialog, as follows.

Calculate from the protein structure

In the PDB options tab in the File open options dialog, There is the checkbox of Calculate protein secondary structure. When this checkbox is turned ON, the protein secondary structure will be calculated from the atomic coordinates using the DSSP algorism.

Read from the definition in the PDB file

In contrast, when this checkbox is turned OFF,the secondary structure will be assigned from the HELIX/SHEET records defined in the PDB file. In the case of the mmCIF and other formats, it will be assigned from the corresponding records. Files downloaded from the web sites (RCSB site, etc.) usually contain these records, while PDB files created from other modeling programs sometimes lack these records. In such cases, no secondary structures will be assigned, and thus ribbon and cartoon renderer will be incorrectly displayed.

Re-assignment of secondary structures

After opening the molecular coordinates files (PDB, etc.), you can re-assign secondary structures manually.

By executing the menu, "Tools" --> "Reassign secondary str...", you will see the following “Protein secondary str tool” dialog box.

Manual assignment of secondary structures

When you select the Assign by selection of the radio buttons, the tool enters the manual assignment mode. In this manual assignment mode, you can change the secondary structure definition of the target region of the molecule, as follows.

1. Enter the selection syntax corresponding to the target region in the “Selection” box. (It may be useful to select the target region using other selection GUIs before opening this dialog box, since the current selection will be appeared as default in this selection box.)
2. Select the type of the secondary structure you want to assign in the “Type” listbox.
3. Push the OK button and then the secondary structure will be changed.

In the Type listbox, you can choose the five types (i.e., coil, β strand, α, 3-10, and π helices) of the secondary structure. However, in both ribbon and cartoon renderers, all of the helices (α, 3-10, and π) are displayed as the helical segment. (So, setting helix type other than α helix will be meaningless...)

CAUTION:

You can assign inconsistent secondary structures to the actual protein structure, using this manual assignment function. However, such inconsistent assignments result in a strange display of ribbon or cartoon, and extremely inconsistent assignments possibly result in the crash of the application. So, it may be better to save the scene to the QSC file, before changing the secondary structure manually.

The figure below shows the crambin structure (1CRN), after changing its secondary structure inconsistently (i.e., changing all residues to a β strand). The representation becomes completely dissimilar to the actual main chain structure, so such display is meaningless and should be avoided.

Re-calculation of the secondary structure from the coordinates

When you select the Recalc secondry str of the radio buttons, the tool enters the “Re-calculation” mode. In this mode, the secondary structure is calculated from the atomic coordinates using the DSSP algorism. Although the algorism is the same as the automatic assignment performed on opening the PDB (and other format) files, tou can specify the additional options, which are only available in this re-calculation dialog box.

Ignore β bulge

When this option is turned ON, the β bulge regions are assigned as coils. Otherwise, they will be assigned as β strands. Assignment of a β bulge as a β strand sometimes results in a strangely kinked β sheet (left fig, below). To avoid this, you may want to turn on this option (right fig, below).

Helix gap-fill angle (°)

When this option is turned ON, short coil regions between helices (helix gap) are assigned as helix. Especially, when you show helical proteins by the cartoon renderer, you may find that a single helical segment is shown as several discontinuous small helices (cylinders). To avoid it, you can recaluculate the secondary structure using this option. in this option, You can specify the parameter angle of 0~180°, Which determines how much deviation from a straight helix is allowed in filling the gap. A larger angle value results in a more bent helical regions, whereas 0° results in the same as this option turned off (i.e., no helix-gap will be filled).

Left: helix gap-fill OFF, Middle: helix gap-fill ON (angle=55°), Right: helix gap-fill ON (angle=120°)

Other topics

Saving the scenes containing molecules with the re-assigned secondary structures

When you save the scenes containing molecules whose secondary structures are modified (re-assigned/re-calculated above methods), the molecular (MolCoord) objects are automatically embedded in the QSC file. In this QSC file, the modified secondary structures are also recorded, and so you can reproduce the modified secondary structures across the different sessions of the application (i.e., after quitting and restarting the application).

Undo/redo of the secondary structure modification

All of the above modification of the secondary structures (re-assigned/re-calculated above methods) are undo/redo-able. If you found that you wrongly changed the secondary structure assignment, You can restore the original state before changing the secondary structure by the undo command (ref?).