Enhanced Entrez
Cn3D 2.5
| Cn3D
2.5 Offers Feature Editing and Global Save |
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| NCBI
has recently released version 2.5 of the Cn3D macromolecular structure
viewer. PC users will enjoy a smooth, single-click installation process
and all users will appreciate the usability enhancements in this latest
release. Cn3D 2.5 offers a greatly expanded array of annotation tools, including the ability to define molecular features and specify their display characteristics. Greater control over every aspect of the molecular display is facilitated through four control panels, which govern molecular color schemes, visibility, rendering, and labeling. After a molecule, or set of molecules, has been rendered and annotated, the entire ensemble of coordinate data and display specifications can be saved for later viewing or transmittal to colleagues. These new annotation features are illustrated below, based on an example from the online Cn3D tutorial. Figure 1 shows the area of the active site of two structurally aligned 5´-3´ exonucleases. The structural alignment was produced by NCBI’s Vector Alignment Search Tool
(VAST) and downloaded by Cn3D from the Molecular Modeling Database (MMDB). The dark-colored residues are those of the bacteriophage T4 enzyme with PDB code “1TFR,”1 and the light-colored residues are those of the T5 enzyme with PDB code “1EXN.”2 The two dark spheres represent catalytically important magnesium ions present in the 1TFR structure. The 1TFR and 1EXN exonucleases are responsible for removing RNA primers used during bacteriophage DNA replication. |
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To generate this view, the alpha carbon traces of the default Cn3D Neighbor representation have been turned off, and two groups of amino acids have been defined as “Features” and independently rendered as “fat tubes.” This rendering mode reveals the excellent alignment of the corresponding side chains in the two structures. The background color was also changed from its default of black to gray, another new option in Cn3D 2.5, using the Options menu. Features were defined and given independent rendering and visibility settings using the Viewer Controls window. To define the feature “t4_cat,” for instance, 1TFR residues D19, D71, D132, and D155 were first selected in the Sequence window. The Feature panel of the Viewer Controls window, shown in Figure 2, was then used to give the selected residues a feature name and define their display and visibility properties. The alignment, rendering settings, and user-defined features, “t4_cat” and “t5_cat,” can be saved in a single file for later retrieval by using the new Global Save function provided by the File/Save/All menu option. Cn3D is a project of NCBI’s Molecular Structure research group, headed by Steve Bryant. The new features in release 2.5 were developed primarily by NCBI scientists Yanli Wang, Lewis Geer, Colombe Chappey, and Jonathan Kans. To download or read more about Cn3D, visit www.ncbi.nlm.nih.gov/Structure/CN3D. —DW,
YW
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