BioStruct3DView pluginBioStruct3DView plugin is 3D molecular protein and DNA structure viewer. OverviewBiostruct3DView plugin is intended for visualization of biological maromolecular 3d structures (DNA, RNA and proteins). To run the viewer you need a file that contains 3D structure data. Unipro UGENE v1.4 supports following formats:
Viewer Features:Basic usageOpening a PDB or MMDB ASN.1 file will automatically activate BioStruct3DView plugin. Also dobule clicking on object associated with PDB file (3D model, sequence or annotation) will activate the viewer. You can download remote PDB molecule by id using menu File->Download PDB molecule You can rotate 3d model using left mouse button and zoom in/out using mouse wheel. Also you can control the model using toolbar buttons Zoom In, Zoom Out and Restore Default View. To activate an anaglyph mode, click the anaglyph view checkbox in the settings dialog. You can change images shift by moving the slider, and anaglyph glasses color by selecting a color preset or manually by clicking on left or right color. With the help of toolbar menu Links you can retrieve additional structure information directly from Web. This is customizable menu, check out file 'BioStruct3DLinks.txt' from UGENE data/biostruct3d_plugin folder for details. On the picture below you see BioStruct3D viewer on the top. The Display menu includes such features as rendering style, coloring schema, background color, image export and spin animation. You can also activate Display menu as context using right mouse button click in the model view.
 You can export 3d view image to one of supported formats: SVG, PostScript, PNG, JPEG. Customize the image using controls and command Display->Set background color. When you select a part of a sequence (using mouse drug or context menu Select->Sequence Region) or any annotation in sequence viewer window,
the selection will also be highlighted in the 3D model view. For example, you can see below the yellow coloring of the selection region 1-54. Also you can add your own annotations as well.
 Views and models Several 3d views can be added to the render window using 'Add' dialog from toolbar or drag-and-drop from Project Tree view. All views will be rendered independently.
 When structure has multiple models you can navigate among them using Display->Models menu. You can draw all of them instantly using Models->All models command.
 Also one can calculate and visualize moleuclar surface via BioStruct3D. This can be done using Display->Molecular surface menu. Right now Van-der-Waals surface is supported, but other surface type support is planned in next releases.
 Upcoming featuresThese are planned to be implemented in next releases:- Active sites and ligands search - NCBI MMDB binary format support And these are long-term development plans:
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