POLYVIEW-3D server generates animated images as well as publication quality static slides of protein 3D structures using the PDB formatted data. For details, please refer to POLYVIEW-3D documentation.

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Settings (Click on Samples links to see respective examples) Protein structure info (Help, Samples) Data Source: PDB deposited data PDB ID  considered as Asymmetric unit Biological unit (PQS) Get ID by keyword Custom PDB formatted data File  Specify the source in Structure annotation option set Model number Show ligands as Spheres Sticks Show solvent Initial orientation dX  dY  dZ  Center of view (e.g. A:150 or B: or :30) Image info (Help, Samples) Type of request Single slide Animation Rendering program PyMol RasMol Annotations by POLYVIEW-2D Preview area Available with PDB codes only Extended settings (Help) (Click checkbox to open the respective set of settings) Image Settings Residue Highlighting Tips Animation Settings Chain Color and Rendering Structure annotation Image settings (Help, Samples) Size (NxN pixels) 50 100 150 200 250 300 400 500 600 800 1000 Zoom (%) 100 125 150 175 200 225 250 275 300 Background color Sample Pick color Animation settings (Help, Samples) (To enable settings choose Animation request in the Image info option set) Delay (in 1/100s) Animate Rotation Models Zoom HD slides Rotation settings Angle step Axes of rotation X  Y  Z  Rocking with angle range Model settings Use All available First defined models Zoom settings Final scale 100 125 150 175 200 225 250 275 300 using increment Highlighting (Help, Samples) Individual residues (Example: 1:R,3,A:5-8:g,B:10-13,20:bs,23:f or use list Converter): Residues with interchain contacts to be shown Colored in red With side chains As spheres (for complexes only) Residues by conservation with score > = < 9 (most conserved) 8 7 6 5 4 3 2 1 0 (least conserved) to be shown Colored in red With side chains As spheres Add labels to highlighted residues (RasMol only) Coloring and Rendering (Help, Samples) Press the + button to customize another chain Render rest chains as Cartoons Wire frame CPK spacefill Surface (PyMol) Transparent (PyMol) Hidden colored By chain By atom type By B-factor By conservation By interaction By hydrophilicity By acidity By spectrum By secondary structure All in same color Pick color Advanced Structure Annotation (Help, Samples) Automatically generate results in order to Find pockets using CASTp Render pockets with area with volume all greater than Determine families using Pfam Determine TM domains using PDBTM Map interacting sites found in PDB None of the above Contrast with SPPIDER Submit already generated custom PDB file containing Interface prediction from SPPIDER Functional regions from ConSurf Docking models in CAPRI format overlaid with SPPIDER Trajectories and distortions (e.g. AD-ENM, MolMovDB) Other Options are available with custom PDB files only E-mail address (optional)

The POLYVIEW-3D protein structure visualization server was developed by A.Porollo and J.Meller