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cuemol2/Prot2ndryStrCueMol: Molecular Visualization Framework |
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Protein secondary structure assignmentThe 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 fileThe 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 structureIn 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 fileIn 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 structuresAfter 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 structuresWhen 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.
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:
Re-calculation of the secondary structure from the coordinatesWhen 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.
Other topicsSaving the scenes containing molecules with the re-assigned secondary structuresWhen 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 modificationAll 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?). |