"I see in 3D" (iCn3D) Structure Viewer is a WebGL-based 3D viewer using Three.js and jQuery. iCn3D synchronizes the display of 3D structure, 2D interaction, and 1D sequences and annotations. Users' custom display can be saved in a short URL or a PNG image. Complete package of iCn3D including Three.js and jQuery can be downloaded from https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.16.2.zip. The "Download ZIP" link in this page does not include third-party libraries.
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View a 3D structure in iCn3D: Open the link https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html, input a PDB ID, and click "Load". You can also click "File" menu to "Open File" or input other IDs.
As mentioned in the menu "Help > Transformation Hints", you can use Left mouse button for rotation, Middle mouse wheel for zooming, and Right mouse button for translation.
The most important point about using iCn3D is the current selection. Any operations on color, style, etc. are working on the current selection. By default, all atoms are selected. Once you select any subset, your operation will work ONLY on the subset. You can switch the selection using the toggle next to the Help menu.
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Create custom 3D view: You first open a structure in "File" menu, then select a subset in "Select" menu, view only the selected subset by clicking "View Only Selection" in View menu, finally change styles or colors in "Style" and "Color" menus.
Each operation has a corresponding command as listed at https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.html#commands. These commands will show up in the command/log window right beneath the 3D display. To view all previous commands, you can click "Share Link" in "File" menu. Both the original URL and the short URL can be used to display your custom view.
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Save your work: You can save "iCn3D PNG Image" in the menu "File > Save Files". Both the PNG file and an HTML file are saved. Click the HTML file to see the PNG image, which is linked to the custom display via a shorten URL. The downloaded "iCn3D PNG Image" itself can also be used as an input in the menu "File > Open File" to reproduce the custom display. You can combine these HTML files to generate your own galleries.
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Show binding site: You can click "Chem. Binding" in "View" menu to show all hydrogen bonds around chemicals. You can also click "H-Bonds & Interactions" in "View" menu to list or highlight each hydrogen bond or contact.
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Export models for 3D printing: You can click "3D Printing" in "File" menu to export models for 3D printing. Both STL and VRML files are supported.
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Show transmembrane proteins: If the protein is a transmembrane protein, you can click "File > Retrieve by ID > OPM PDB ID" to input a PDB ID to view the membranes.
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Show surface, EM map, or electron density map: You can click "Style > Surface Type", "Style > EM Density Map", or "Style > Electron Density".
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View 1D sequences and 2D interactions: In the page https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?mmdbid=1TUP, you can click in "Windows" menu to "View Sequences & Annotations", "View Interactions", and see all "Defined Sets", which can be clicked to see any of your selections.
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Select on 3D, 1D and 2D: To select on 3D structures: hold "Alt" and use mouse to pick, hold "Ctrl" to union selection, hold "Shift" to select a range, press the up/down arrow to switch among atom/residue/strand/chain/structure. Click "Save Selection" in "Select" menu to save the current selection.
To select on 1D sequences: drag on the sequences or the blue track title to select.
To select on 2D interaction diagram: click on the nodes or lines. The nodes are chains and can be united with the Ctrl key. The lines are interactions and can NOT be united. Each click on the lines selects half of the lines, i.e., select the interacting residues in one of the two chains.
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Align two structures, align two chains, or align a protein sequence to a structure: You can click "File > Align" to see all three alignment options. You can also realign a subset of the structures.
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Add custom tracks: You can add custom tracks in various formats (FASTA, bed file, etc.) in the annotation window by clicking the menu "Windows > View Sequences & Annotations".
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Show force-directed graph for interactions: You can show the interactions using 2D force-directed graph in the menu "View > H-Bonds & Interactions > 2D Graph (Force-Directed)".
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Calculate and show Solvent accessible surface area (SASA): You can color structures with SASA, or show the SASA for each residue.
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Show symmetry: You can show symmetry when available.
iCn3D can be embedded in a web page by including the URL in HTML iframe, e.g. <iframe src="https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?mmdbid=1tup&width=300&height=300&showcommand=0&mobilemenu=1&showtitle=0" width="320" height="320" style="border:none"></iframe>. This method always shows the most recent version of iCn3D.
To embed iCn3D with JavaScript libraries, the following libraries need to be included: jQuery, jQuery UI, Three.js, and iCn3D library. An html div tag to hold the 3D viewer is added. The iCn3D widget is initialized with the custom defined parameter "cfg": "var icn3dui = new iCn3DUI(cfg); icn3dui.show3DStructure();". Multiple iCn3D widgets can be embedded in a single page. Please see the source code of the example page for reference.
Users can choose to show the most recent version of iCn3D, or a locked version of iCn3D. To show the most recent version, use the library files without the version postfix as shown in the iCn3D Web API page. To show a locked version, use the library files with the version postfix as shown in the source code of iCn3D page. If the input is provided as an MMDB ID, both library files and backend cgis are versioned so that the 3D display will be stable.
iCn3D accepts the following IDs:
- mmdbid: NCBI MMDB ID, e.g., https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?mmdbid=1tup&showanno=1&show2d=1&showsets=1
- mmtfid: MMTF ID, e.g., https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?mmtfid=1tup&show2d=1&showsets=1
- pdbid: PDB ID, e.g., https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?pdbid=1tup&show2d=1&showsets=1
- opmid: Orientations of Proteins in Membranes(OPM) PDB ID, e.g., https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?opmid=6jxr&show2d=1&showsets=1
- mmcifid: mmCIF ID, e.g., https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?mmcifid=1tup&show2d=1&showsets=1
- gi: NCBI protein gi number, https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?gi=827343227&show2d=1&showsets=1
- cid: PubChem Compound ID, e.g., https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?cid=2244
- align two structures: two PDB IDs or MMDB IDs for structure alignment, e.g., https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?align=1hho,4n7n&showalignseq=1&show2d=1&showsets=1
- align two chains: any two chains for structure alignment, e.g., https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?chainalign=1HHO_A,4N7N_A&showalignseq=1&show2d=1&showsets=1
- blast_rep_id and query_id: NCBI protein accessions of a protein sequence and a chain of a 3D structure for sequence-structure alignment, e.g., [https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?from=icn3d&blast_rep_id=1TSR_A&query_id=NP_001108451.1&command=view annotations; set annotation cdd; set annotation site; set view detailed view; select chain 1TSR_A; show selection](https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?from=icn3d&blast_rep_id=1TSR_A&query_id=NP_001108451.1&command=view annotations; set annotation cdd; set annotation site; set view detailed view; select chain 1TSR_A; show selection)
iCn3D also accepts the following file types: PDB, mmCIF, Mol2, SDF, and XYZ. The files can be passed through a url, e.g., https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?type=pdb&url=https%3A%2F%2Ffiles.rcsb.org%2Fview%2F1gpk.pdb. See the help page or the API page for more details.
- jQuery and jQuery UI: used as a general tool to write Javascript code. Some jQuery UI features are used.
- Three.js: used to set up the 3D view.
- D3.js: used to draw force-directed graph .
- iview: The drawing of 3D objects is based on iview.
- GLmol: The drawing of nucleotides cartoon is based on GLmol.
- 3Dmol: The surface generation and labeling are based on 3Dmol.
- NGL Viewer: The Imposter shaders are based on NGL Viewer.
- LiteMol: The parser of EM density data from PDBe is based on LiteMol.
- Orientations of Proteins in Membranes (OPM): The membrane data of transmembrane proteins are from OPM.
- Force-Directed Graph: "2D Graph (Force-Directed)" in the menu "View > H-Bonds & Interactions" is based on Force-Directed Graph.
If you want to build your code easily, you'll need to install nodejs and npm.
Next, clone this repository, and then perform the following setup steps in your working copy of icn3d.
npm install -g gulp
npm install
The first line installs the gulp build tool globally, making the gulp command available on the command line. The next two lines installs all of the dependences for this project.
You only have to perform the above steps once, to set up your working directory. From then on, to build, simply enter:
gulp
Please send all comments to [email protected].
To cite iCn3D, please reference:
Wang J, Youkharibache P, Zhang D, Lanczycki CJ, Geer RC, Madej T, Phan L, Ward M, Lu S, Marchler GH, Wang Y, Bryant SH, Geer LY, Marchler-Bauer A. iCn3D, a Web-based 3D Viewer for Sharing 1D/2D/3D Representations of Biomolecular Structures. Bioinformatics. 2019 June 20; pii: btz502. doi: 10.1093/bioinformatics/btz502. PubMed PMID: 31218344, Full Text at Oxford Academic