| iCn3D | Menu
|
| iCn3D |
| Parameter | Description |
|---|---|
| mmdbafid | A list of PDB or AlphaFold UniProt IDs for realignment, e.g., https://www.ncbi.nlm.nih.gov/Structure/icn3d/?mmdbafid=1HHO,4N7N,P69905,P01942. You could then input multiple PDB files with the menu "File > Open File > PDB Files (appendable)". Next you could click the menu "File > Realign Selection > by Structure Alignment" to realign all loaded structures. |
| mmdbid | NCBI MMDB ID or PDB ID, e.g., ?mmdbid=1tup&showanno=1&show2d=1 |
| mmtfid | MMTF ID, e.g., ?mmtfid=1tup |
| pdbid | PDB ID, e.g., ?pdbid=1tup |
| mmcifid | mmCIF ID, e.g., ?mmcifid=1tup |
| gi | NCBI protein gi number, e.g., ?gi=827343227 |
| cid | PubChem Compound ID, e.g., ?cid=2244 |
| blast_rep_id | NCBI protein accession of a chain of a 3D structure. "blast_rep_id" combines with the parameter "query_id" of a protein sequence to show the sequence-structure alignment, e.g., from=icn3d&blast_rep_id=1TSR_A&query_id=NP_001108451.1 |
| align | Two PDB IDs or MMDB IDs for structure alignment, e.g., ?align=1hho,4n7n |
| chainalign | Two chains for structure alignment, e.g., ?chainalign=1HHO_A,4N7N_A |
| url | Use the url (encoded) to retrieve the 3D structure. The url requires another parameter "type", e.g., ?type=pdb&url=https%3A%2F%2Ffiles.rcsb.org%2Fview%2F1gpk.pdb |
| width | Width of the structure image. It can be percentage such as '100%', or pixel values such as 400. The default is "100%". |
| height | Height of the structure image. It can be percentage such as '100%', or pixel values such as 400. The default is "100%". |
| resize | Set "true" or "1" to resize the image when the container is resized. The default is "true". |
| rotate | Set "right", "left", "up", or "down" to rotate the structure when it is displayed at the beginning. The default is "right". |
| showanno | Set "true" or "1" to show annotations, such as SNPs, ClinVar, domains, binding sites. The default is "false". |
| showalignseq | Set "true" or "1" to show the aligned sequence window. The default is "false". |
| showsets | Set "true" or "1" to show the defined sets. The default is "false". |
| show2d | Set "true" or "1" to show the 2D interaction. The default is "false". |
| showlogo | Set "false" or "0" to hide the NCBI logo at the top of the page. The default is "true". |
| showmenu | Set "false" or "0" to hide the menus and buttons at the top of the structure canvas. The default is "true". |
| showtitle | Set "false" or "0" to hide the title at the top of the structure canvas. The default is "true". |
| showcommand | Set "false" or "0" to hide the command window. The default is "true". |
| mobilemenu | Set "true" or "1" to show the mobile-style menu. Users can click to see all menus. The default is "false". |
| imageonly | Set "true" or "1" to show an image instead of interactive 3D viewer. The default is "false". |
| closepopup | Set "true" or "1" to close the dialogs of "Defined Sets", "Interactions", and "Sequences and Annotations". The default is "false". |
| command | Besides the "Script/Log" section at the bottom of the canvas, commands can also be attached to the url parameter "command". The easy way to generate the commands is to operate manually to get your custom display and then click "File > Share Link" to find the URL with full commands or just the short URL. |
| replay | Set "true" or "1" to replay each step of a custom display. |
| usepdbnum | Set "true" or "1" to use PDB residue numbers instead of NCBI residue numbers when the input is MMDB ID and the residue numbers are different. The default is "true". |
| hidelicense | Set "true" or "1" to hide the features requiring licenses, such as "Analysis > DelPhi Potential". The default is "false". |
| shownote | Set "true" or "1" to show the content in "Analysis > Window Title" as the window title. The default is "false". |
| menuicon | Set "true" or "1" to show icons for those menus requiring internet or license. The default is "false". |
| Menu | Command | Description |
| File > Search Structure > PDB Structures | N/A | Search PDB structures at NCBI Structure page |
| File > Search Structure > AlphaFold Structures | N/A | Search AlphaFold structures with AlphaFold ID, protein names, or gene names |
| File > Search Structure > AlphaFold UniProt Database | URL: https://alphafold.ebi.ac.uk/ | Search AlphaFold structures at AlphaFold UniProt Database |
| File > Search Similar > NCBI VAST+ (PDB Complex) | URL: https://www.ncbi.nlm.nih.gov/Structure/vastplus/vastplus.cgi?uid=6VXX | Search similar PDB complexes with the tool VAST+ |
| File > Search Similar > NCBI VAST (PDB Chain) | URL: https://www.ncbi.nlm.nih.gov/Structure/vast/vastsrv.cgi?pdbid=4N7N&chain=A | Search similar PDB chains with the tool VAST |
| File > Search Similar > Foldseek (PDB & AlphaFold) | https://search.foldseek.com/ | Search similar PDB and AlphaFold structures with the tool Foldseek |
| File > Retrieve by ID > PDB/MMDB/AlphaFold IDs | load mmdbaf0 1GPK,P69905 or URL parameter: &mmdbafid=1GPK,P69905 |
Load a list of comma-separated PDB IDs, MMDB IDs, or AlphaFold IDs |
| File > Retrieve by ID > AlphaFold Structures > NCBI Protein Accession | load refseq NP_001743.1 or URL parameter: &refseqid=NP_001743.1 |
Load an AlphaFold structure with an NCBI protein accession |
| File > Retrieve by ID > RCSB mmCIF ID | load mmcif pdb_00001tup or URL parameter: &mmcifid=pdb_00001tup |
Load a structure with an RCSB mmCIF ID |
| File > Retrieve by ID > PubChem CID/Name/InChI | load cid 2244 or URL parameter: &cid=2244 |
Load a compound with PubChem CID, name, or InChI |
| File > Retrieve by ID > Chemical SMILES | load smiles CC(=O)OC1=CC=CC=C1C(=O)O or URL parameter: &smiles=CC(%3DO)OC1%3DCC%3DCC%3DC1C(%3DO)O |
Load a compound with SMILES |
| File > Open File > PDB Files (appendable) | N/A | Open one or more PDB files |
| File > Open File > mmCIF Files (appendable) | N/A | Open one or more mmCIF files |
| File > Open File > SDF File | N/A | Open one chemical SDF file |
| File > Open File > MD Trajectory File | N/A | Open one MD trajectory file (DCD or XTC) |
| File > Open File > Multiple Seq. Alignment > CLUSTALW Format | N/A | Open one multiple sequence alignment file in CLUSTALW format to show the MSA and the structural alignment |
| File > Open File > Multiple Seq. Alignment > FASTA Format | N/A | Open one multiple sequence alignment file in FASTA format to show the MSA and the structural alignment |
| File > Open File > AlphaFold PAE File | N/A | Open one AlphaFold PAE (Predicted Aligned Error) file to show the PAE heatmap |
| File > Open File > iCn3D PNG (appendable) | N/A | Open one or more iCn3D PNG files |
| File > Open File > Selection File | N/A | Open one iCn3D selection file with defined sets such as "1TUP_A select .A:94-289" |
| File > Open File > Collection File | N/A | Open one iCn3D collection file with a list of IDs. The examples are at https://github.com/ncbi/icn3d/tree/master/example/collection. |
| File > Open File > Electron Density > Local File | N/A | Open one local electron density map file in CCP4 or MTZ format |
| File > Open File > Predict by Seq. > ESMFold | N/A | Predict a structure from a protein sequence with the tool ESMFold |
| File > Align > Multiple Chains > by Structure Alignment | URL: https://www.ncbi.nlm.nih.gov/Structure/icn3d/?chainalign=P69905_A,P01942_A,1HHO_A&aligntool=tmalign | Align a list of comma-separated PDB chains (e.g., 1HHO_A) or AlphaFold IDs (e.g., P69905) with the tool TM-align or VAST align. This is different from aligning two structures. |
| File > Align > Multiple Chains > by Sequence Alignment | URL: https://www.ncbi.nlm.nih.gov/Structure/icn3d/?chainalign=P69905_A,P01942_A,1HHO_A&resnum=1-10,20-50&showalignseq=1 | Align a list of comma-separated PDB chains (e.g., 1HHO_A) or AlphaFold IDs (e.g., P69905) based on a list of residue numbers (e.g., 1-10,20-50) in the first chain |
| File > Align > Multiple Chains > Residue by Residue | URL: https://www.ncbi.nlm.nih.gov/Structure/icn3d/?chainalign=P69905_A,P01942_A,1HHO_A&resdef=1,5,10-50 | 1,5,10-50:+2,6,11-51 | 1,5,10-50&showalignseq=1 | Align a list of comma-separated PDB chains (e.g., 1HHO_A) or AlphaFold IDs (e.g., P69905) based on a list of ":+"-separated residue mapping (e.g., 1,5,10-50 | 1,5,10-50, where " | " is used to separate the residues in the first chain and in the current chain) for each pair of chains |
| File > Align > Protein Complexes > Two PDB Structures | URL: https://www.ncbi.nlm.nih.gov/Structure/icn3d/?align=2DN3,4N7N | Align two PDB structures with the tool VAST+. This is different from aligning two chains. |
| File > Align > Sequence to Structure | URL: https://www.ncbi.nlm.nih.gov/Structure/icn3d/?from=icn3d&alg=blast&blast_rep_id=1TSR_A&query_id=NP_001108451.1 | Show the sequence alignment of a protein sequence with a PDB chain using BLAST in the context of 3D structure |
| File > Realign Selection > Multiple Chains > by Structure Alignment | realign on tmalign | 1HHO_A,P01942_A,P69905_A | Realign the selected list of comma-separated PDB chains (e.g., 1HHO_A) or AlphaFold IDs (e.g., P69905) with the tool TM-align or VAST align |
| File > Realign Selection > Multiple Chains > by Sequence Alignment | realign on seq align | 1HHO_A,P01942_A,P69905_A | Realign the selected list of comma-separated PDB chains (e.g., 1HHO_A) or AlphaFold IDs (e.g., P69905) based on the sequence alignment with the tool BLAST |
| File > Realign Selection > Multiple Chains > Residue by Residue | realign predefined P69905_A,P01942_A,1HHO_A 1,5,10-50 | 1,5,10-50:+2,6,11-51 | 1,5,10-50 | Realign the selected list of comma-separated PDB chains (e.g., 1HHO_A) or AlphaFold IDs (e.g., P69905) based on a list of ":+"-separated residue mapping (e.g., 1,5,10-50 | 1,5,10-50, where " | " is used to separate the residues in the first chain and in the current chain) for each pair of chains |
| File > Realign Selection > Protein Complexes | realign on vastplus | 1HHO,P01942 | Realign the selected list of structures with the tool VAST+ |
| File > 3D Printing > WRL/VRML (Color, W/ Stabilizers) | export vrml stabilizer file | Export the current 3D structure in WRL/VRML file format with original color for 3D printing |
| File > 3D Printing > STL (W/ Stabilizers) | export stl stabilizer file | Export the current 3D structure in STL file format with black/white color for 3D printing |
| File > Save File > iCn3D PNG Image > Original Size | export canvas | Export the canvas as an iCn3D PNG image with all involved commands appended at the end of the PNG file |
| File > Save File > iCn3D PNG Image > 4X Large | export canvas 4 | Export the canvas as an 4 times large iCn3D PNG image with all involved commands appended at the end of the PNG file |
| File > Save File > Video | N/A | Export the canvas as a MP4 video as the structure changes its orientation by the user or automatically |
| File > Save File > Selection File | N/A | Export the current defined sets in a selection file. Each set contains the name and the selection command, e.g., "1TUP_A select .A:94-289". |
| File > Save File > PDB | export pdb | Export the current 3D coordinates in a PDB file |
| File > Save File > Secondary Structure | export secondary structure | Export the secondary structure and residue number information in a JSON file |
| File > Share Link | N/A | Generate a URL with all commands, a shortened URL, and commands used in Jupyter Notebook. |
| Select > Defined Sets | defined sets | Show all defined sets to make a selection |
| Select > All | select all | Select all atoms of the structures |
| Select > Displayed Set | select displayed set | Select all atoms currently displayed |
| Select > by Distance | select zone cutoff [cutoff value in angstrom] | Select all residues within a certain distance from the current selection |
| Select > by Property > Positive | select prop positive | Select all positively charged residues (Arg, Lys, and His) for the current selection |
| Select > by Property > Negative | select prop negative | Select all negatively charged residues (Asp and Glu) for the current selection |
| Select > by Property > Hydrophobic | select prop hydrophobic | Select all hydrophobic residues (Val, Leu, Ile, Met, Phe, Tyr, Trp, and Cys) for the current selection |
| Select > by Property > Polar | select prop polar | Select all polar residues (Ser, Thr, Asn, Gln, Pro, Ala, and Gly) for the current selection |
| Select > by Property > B-factor/pLDDT | select prop b factor | 90_100 | Select all residues with B-factor or pLDDT value in a certain range (e.g., 90_100) for the current selection |
| Select > by Property > Solvent Accessibility | select prop percent out | 0_50 | Select all residues with solvent accessibility in a certain range (e.g., 0_50) for the current selection |
| Select > Inverse | select complement | Select all atoms not in the current selection |
| Select > Main Chains | select main chains | Select the main chain atoms (C-alpha, C, N, and O) for the current selection |
| Select > Side Chains | select side chains | Select the side chain atoms (i.e., all atoms except main chain atoms) for the current selection |
| Select > Advanced | select [specification] | name [name of the set] | Use a simple specification (e.g., $1HHO.A:5-10@CA) specified at https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.html#selectb to select a set of atoms and name the set |
| Select > Select on 3D > Chain | set pk chain | Press the Alt key and click on 3D structure to select a chain |
| Select > Select on 3D > Strand/Helix | set pk strand | Press the Alt key and click on 3D structure to select a secondary structure (strand or helix) |
| Select > Select on 3D > Residue | set pk residue | Press the Alt key and click on 3D structure to select a residue |
| Select > Select on 3D > Atom | set pk atom | Press the Alt key and click on 3D structure to select an atom |
| Select > Save Selection | select [specification] | name [name of the set] | Save the current selection with a name in the Defined Sets menu |
| Select > Clear Selection | clear all | Reset the selection to all atoms |
| Select > Highlight Style > Outline | set highlight style outline | Set the highlight style as outline |
| Select > Highlight Style > 3D Objects | set highlight style 3d | Set the highlight style as 3D objects (e.g., cubes) |
| Select > Toggle Highlight | toggle highlight | Toggle between the current selection and all atoms |
| View > View Selection | show selection | View only the current selection |
| View > Hide Selection | hide selection | Hide the current selection |
| View > Zoom in Selection | zoom selection | Zoom into the current selection |
| View > Center Selection | center selection | Set the current selection to the center |
| View > Alternate(Key "a") | N/A | Alternate the structures one by one |
| View > Stereo View > On | stereo on | Turn on stereo view |
| View > Stereo View > Off | stereo off | Turn off stereo view |
| View > Side by Side | URL: https://www.ncbi.nlm.nih.gov/Structure/icn3d/full2.html?... | Show the first structure in the first window and the second (if available, otherwise the same structure) in the second window to compare side by side. THis is achieved by replace "icn3d/?" or "icn3d/full.html?" with "icn3d/full2.html?". |
| View > Rotate > Auto Rotation > Rotate Left | rotate left | Rotate the structure continuously to the left until a mouse click is made |
| View > Rotate > Auto Rotation > Rotate Right | rotate right | Rotate the structure continuously to the right until a mouse click is made |
| View > Rotate > Auto Rotation > Rotate Up | rotate up | Rotate the structure continuously upward until a mouse click is made |
| View > Rotate > Auto Rotation > Rotate Down | rotate down | Rotate the structure continuously downward until a mouse click is made |
| View > Fog for Selection > On | set fog on | Set fog on for the current selection to hide objects in the back |
| View > Fog for Selection > Off | set fog off | Set fog off for the current selection to show objects in the back |
| View > Slab for Selection > On | set slab on | Set slab on for the current selection to hide objects in the front |
| View > Slab for Selection > Off | set slab off | Set slab off for the current selection to show objects in the front |
| View > XYZ-axes > Original | set axis on | Show the original XYZ axes |
| View > XYZ-axes > Prin. Axes on Sel. | set pc1 axis | Show the principal axes for the current selection |
| View > XYZ-axes > Hide | set axis off | Remove the axes |
| View > Reset > All | reset | Reset everything to the default |
| View > Reset > Orientation | reset orientation | Reset just the orientation of the structures |
| View > Full Screen | N/A | Show the canvas in full screen mode |
| Style > Protein > Ribbon | style proteins ribbon | Show the secondary structures of proteins as ribbon and coils as thin tubes |
| Style > Protein > Strand | style proteins strand | Show the secondary structures of proteins as six curves and coils as thin tubes |
| Style > Protein > Cylinder and Plate | style proteins cylinder and plate | Show the helices as cylinders, the strands as ribbons, and coils as thin tubes |
| Style > Protein > Schematic | style proteins schematic | Show each residue in proteins as a single-letter label, and connect the residues with sticks |
| Style > Protein > C Alpha Trace | style proteins c alpha trace | Connect all residues in proteins with sticks through C-alpha atoms |
| Style > Protein > Backbone | style proteins backbone | Show the backbone atoms (C-alpha, C, N, and O) of the proteins as sticks |
| Style > Protein > B-factor Tube | style proteins b factor tube | Connect all residues in proteins with a tube, where the thickness of the tube is proportional to the B-factor or pLDDT value of each residue |
| Style > Protein > Lines | style proteins lines | Show all bonds in proteins as lines |
| Style > Protein > Stick | style proteins stick | Show all bonds in proteins as sticks |
| Style > Protein > Ball and Stick | style proteins ball and stick | Show all atoms in proteins as spheres and all bonds as sticks |
| Style > Protein > Sphere | style proteins sphere | Show all atoms in proteins as spheres |
| Style > Protein > Hide | style proteins nothing | Hide the proteins |
| Style > Side Chains > Lines | style sidec lines | Show all bonds in side chains as lines |
| Style > Side Chains > Stick | style sidec stick | Show all bonds in side chains as sticks |
| Style > Side Chains > Ball and Stick | style sidec ball and stick | Show all atoms as spheres and all bonds as sticks for the side chains |
| Style > Side Chains > Sphere | style sidec sphere | Show all atoms in side chains as spheres |
| Style > Side Chains > Hide | style sidec nothing | Hide the protein side chains |
| Style > Nucleotides > Nucleotide Cartoon | style nucleotides nucleotide cartoon | Show nucleotides as nucleotide cartoon |
| Style > Nucleotides > O3' Trace | style nucleotides o3 trace | Connect all residues in nucleotides with sticks through O3 atoms |
| Style > Nucleotides > Backbone | style nucleotides o3 trace | Show the backbone atoms of the nucleotides as sticks and hide the nucleotide bases |
| Style > Nucleotides > Schematic | style nucleotides schematic | Show each residue in nucleotides as a single-letter label, and connect the residues with sticks |
| Style > Nucleotides > Lines | style nucleotides lines | Show all bonds in nucleotides as lines |
| Style > Nucleotides > Stick | style nucleotides stick | Show all bonds in nucleotides as sticks |
| Style > Nucleotides > Ball and Stick | style nucleotides ball and stick | Show all atoms in nucleotides as spheres and all bonds as sticks |
| Style > Nucleotides > Sphere | style nucleotides sphere | Show all atoms in nucleotides as spheres |
| Style > Nucleotides > Hide | style nucleotides nothing | Hide the nucleotides |
| Style > Nucl. Bases > Lines | style ntbase lines2 | Show all bonds in the bases of nucleotides as lines |
| Style > Nucl. Bases > Stick | style ntbase stick2 | Show all bonds in the bases of nucleotides as sticks |
| Style > Nucl. Bases > Ball and Stick | style ntbase ball and stick2 | Show all atoms as spheres and all bonds as sticks for the bases of nucleotides |
| Style > Nucl. Bases > Sphere | style ntbase sphere2 | Show all atoms in the bases of nucleotides as spheres |
| Style > Nucl. Bases > Hide | style ntbase nothing | Hide the bases of the nucleotides |
| Style > Chemicals > Lines | style chemicals lines | Show all bonds in Chemicals as lines |
| Style > Chemicals > Stick | style chemicals stick | Show all bonds in Chemicals as sticks |
| Style > Chemicals > Ball and Stick | style chemicals ball and stick | Show all atoms in Chemicals as spheres and all bonds as sticks |
| Style > Chemicals > Schematic | style chemicals schematic | Show each non-carbon and non-hydrogen atom in chemicals as a single-letter label |
| Style > Chemicals > Sphere | style chemicals sphere | Show all atoms in Chemicals as spheres |
| Style > Chemicals > Hide | style chemicals nothing | Hide the chemicals |
| Style > Glycans > Show Cartoon | glycans cartoon yes | Show glycans as transparent 3D objects (e.g., cubes, spheres) |
| Style > Glycans > Hide Cartoon | glycans cartoon no | Show glycans as chemicals |
| Style > Ions > Sphere | style ions sphere | Show all ions as spheres |
| Style > Ions > Dot | style ions dot | Show all ions as small spheres |
| Style > Ions > Hide | style ions nothing | Hide the ions |
| Style > Water > Sphere | style water sphere | Show all water as spheres |
| Style > Water > Dot | style water dot | Show all water as small spheres |
| Style > Water > Hide | style water nothing | Hide the water |
| Style > Save Style | save style | Save the current style to be used later |
| Style > Apply Saved Style | apply saved style | Apply the previously saved style to the current selection |
| Style > Surface Type > Van der Waals | set surface Van der Waals surface | Show the Van der Waals surface for the current selection |
| Style > Surface Type > Molecular Surface | set surface molecular surface | Show the molecular surface for the current selection |
| Style > Surface Type > Solvent Accessible | set surface solvent accessible surface | Show the solvent accessible surface for the current selection |
| Style > Remove Surface | set surface nothing | Remove all surfaces |
| Style > Surface Opacity > Fast Transparency | set surface opacity [opacity value] | Set the opacity of the surface for the current selection. The opacity value can be between 0 (fully transparent) and 1 (fully opaque). |
| Style > Surface Wireframe > Yes | set surface wireframe on | Use wireframe to show the surface for the current selection |
| Style > Surface Wireframe > No | set surface wireframe off | Show the regular surface for the current selection |
| Style > Line btw. Two Sets | add line | x1 4.4 y1 2.8 z1 7.3 | x2 7.9 y2 3.4 z2 7.3 | color #ffff00 | dashed false | type cylinder | radius 0.4 | opacity 0.3 | Add a line between two sets specified by the coordinates of the center of masses of the two sets. Additional parameters include color (hex color code), dashed (true/false), radius (for cylinder), and opacity (0 to 1) |
| Style > Plane among 3 Sets | add plane | x1 4.4 y1 2.8 z1 7.3 | x2 7.9 y2 3.4 z2 7.3 | x3 97.9 y3 23.4 z3 07.3 | color #ffff00 | thickness 2 | opacity 0.3 | Add a plane among three sets specified by the coordinates of the center of masses of the three sets. Additional parameters include color (hex color code), thickness, and opacity (0 to 1) |
| Style > Electron Density > 2Fo-Fc Map | set map 2fofc sigma 1.5 | Show the 2Fo-Fc electron density map at a certain sigma level (e.g., 1.5) for crystal structures |
| Style > Electron Density > Fo-Fc Map | set map fofc sigma 3 | Show the Fo-Fc electron density map at a certain sigma level (e.g., 3) for crystal structures |
| Style > Electron Density > Remove Map | setoption map nothing | Remove all electron density maps |
| Style > Map Wireframe > Yes | set map wireframe on | Show the electron density map in wireframe style |
| Style > Map Wireframe > No | set map wireframe off | Show the electron density map as surface |
| Style > EM Density Map | set emmap percentage 30 | Show the EM density map at a certain percentage (e.g., 30) of maximum EM values for Cryo-EM structures |
| Style > Remove EM Map | setoption emmap nothing | Remove all EM density maps |
| Style > EM Map Wireframe > Yes | set emmap wireframe on | Show the EM density map in wireframe style |
| Style > EM Map Wireframe > No | set emmap wireframe off | Show the EM density map as surface |
| Style > Background > Transparent | set background transparent | Set the backgrouond of the canvas to transparent |
| Style > Background > Black | set background black | Set the backgrouond of the canvas to black |
| Style > Background > Grey | set background grey | Set the backgrouond of the canvas to grey |
| Style > Background > White | set background white | Set the backgrouond of the canvas to white |
| Color > Unicolor | color [color name or hex color code] | Color the current selection with a single color specified by the color name (e.g., red, green, blue) or hex color code (e.g., FF0000 for red) |
| Color > Color Picker | color [hex color code] | Color the current selection with a picked color specified by the hex color code (e.g., FF0000 for red) |
| Color > Rainbow (R-V) > for Selection | color rainbow | Color the current selection with a rainbow color scheme from red to violet |
| Color > Rainbow (R-V) > for Chains | color rainbow for chains | Color each chain in the current selection with a rainbow color scheme from red to violet |
| Color > Spectrum (V-R) > for Selection | color spectrum | Color the current selection with a spectrum color scheme from violet to red |
| Color > Spectrum (V-R) > for Chains | color spectrum for chains | Color each chain in the current selection with a spectrum color scheme from violet to red |
| Color > Secondary > Sheet in Green | color secondary structure | Color the secondary structure of the current selection with a color scheme (helix in red, strand in green, coil in light blue) |
| Color > Secondary > Sheet in Yellow | color secondary structure yellow | Color the secondary structure of the current selection with a default color scheme (helix in red, strand in yellow, coil in light blue) |
| Color > Charge | color charge | Color the current selection based on the charge of the residues (positive in blue, negative in red, neutral in gray) |
| Color > Hydrophobicity > Normalized | color normalized hydrophobic | Color the current selection based on the normalized Wimley-White hydrophobicity (https://en.wikipedia.org/wiki/Hydrophobicity_scales) of the residues (hydrophobic in green, hydrophilic in gray) |
| Color > B-factor > Original | color b factor | Color the current selection based on the original B-factor values of the residues (low in blue, high in red) |
| Color > B-factor > Percentile | color b factor percentile | Color the current selection based on the percentile of the B-factor values of the residues (low in blue, high in red) |
| Color > Solvent Accessibility | color area | 35 | Color each residue based on the percentage of solvent accessilbe surface area. The color ranges from blue, to white, to red for a percentage of 0, 35(variable), and 100, respectively. |
| Color > Structure | color structure | Color each structure in the current selection with a different color |
| Color > Chain | color chain | Color each chain in the current selection with a different color |
| Color > 3D Domain | color 3ddomain | Color each 3D domain in the current selection with a different color based on the 3D domain definition in iCn3D |
| Color > Residue > Default | color residue | Color each residue in the current selection with a different default color |
| Color > Atom | color atom | Color each atom in the current selection with a different default color based on the atom type |
| Color > Identity | color identity | For aligned structures, color aligned residues in red if the residues are identical, in blue if the residues are different |
| Color > Conservation | color conservation | For aligned structures, assign the conservation color based on the BLOSUM62 matrix |
| Color > pLDDT | color confidence | Color the current selection based on the pLDDT confidence score of the atoms. Atoms with very high pLDDT (> 90) are colored in blue, high (90 > pLDDT > 70) in light blue, low (70 > pLDDT > 50) in yellow, and very low (pLDDT < 50) in orange. |
| Color > Ig Strand | color ig strand | When Ig domains are identified for the structures, assign the Ig strands (strands A, B, C, C', D, E, F, G) with predefined color. |
| Color > Save Color | save color | Save the current color scheme to be used later |
| Color > Apply Saved Color | apply saved color | Apply the previously saved color scheme to the current selection |
| Analysis > Seq. & Annotations | view annotations | View the sequences and annotations of the current selection in the 1D sequence viewer |
| Analysis > Aligned Seq. | window aligned sequence | View the aligned sequences of the current selection in a separate window |
| Analysis > 2D Diagram > for RNAs > R2DT Diagram | diagram 2d nucleotide | 8SH5_R | View the R2DT diagram, generated by RNACentral, of the chain 8SH5_R in a separate window. |
| Analysis > 2D Diagram > for RNAs > 2D Diagram with RNAcanvas | diagram 2d fr3d | 8SH5_R | View the 2D diagram, generated by RNAcanvas, of the chain 8SH5_R in a separate window. |
| Analysis > 2D Diagram > for Ig Domains | diagram 2d ig | 1CD8_A | View the 2D diagram of the Ig domain in the chain 1CD8_A in a separate window. |
| Analysis > 2D Diagram > for Chains | view 2d diagram | View the 2D diagram of the current selection in a separate window. This command is not required to show the interactions, which can be done via the menu "Analysis > Interactions". |
| Analysis > 2D Cartoon > Chain Level | cartoon 2d chain | Show each chain as an oval with a gradient color for the current selection in a separate window |
| Analysis > 2D Cartoon > Domain Level | cartoon 2d domain | Show each domain as an oval with a gradient color for the current selection in a separate window |
| Analysis > 2D Cartoon > Helix/Sheet Level | cartoon 2d secondary | Show each helix as a filled cylinder and sheet as an empty rectangle for the current selection in a separate window |
| Analysis > Defined Sets | defined sets | View all defined sets to make a selection in a separate window |
| Analysis > Interactions | line graph interaction pairs | [1st set] [2nd set] or line graph interaction pairs | [1st set] [2nd set] | hbonds,salt bridge,interactions,halogen,pi-cation,pi-stacking | false | threshold 3.8 6 4 3.8 6 5.5 |
Show the interactions between two sets in a separate window based on the specified interaction types and thresholds. By default, 2D Interaction Network is used with the prefix "line graph interaction pairs", not "view interaction pairs". |
| Analysis > Contact Map | contact map | dist 8 | type cbeta | Show the contact map for the current selection in a separate window based on the specified distance cutoff (e.g., 8 Angstrom) and atom type (e.g., c-alpha, c-beta, and heavy atoms) |
| Analysis > Mutation | scap interaction [mutation, e.g., 6M0J_E_501_Y] | Please specify the mutations with a comma separated mutation list. Each mutation can be specified as "[uppercase PDB ID or AlphaFold UniProt ID]_[Chain Name]_[Residue Number]_[One Letter Mutant Residue]". E.g., the mutation of N501Y in the E chain of PDB 6M0J can be specified as "6M0J_E_501_Y". For AlphaFold structures, the "Chain ID" is "A". |
| Analysis > DelPhi Potential > DelPhi Potential | set delphi surface or set delphi surface | contour 2 | gsize 65 | salt 0.15 | surface 22 | opacity 1.0 | wireframe no |
Show the DelPhi/electrostatic potential surface for the current selection with the specified contour level (e.g., max potential 2 kT/e), grid size, salt concentration, surface type, opacity, and wireframe option |
| Analysis > Distance > between Two Atoms | add line | x1 44.74 y1 -2.248 z1 95.95 | x2 50.62 y2 -4.272 z2 99.41 | color #ffff00 | dashed true | type distance; add label [label text] | x [x] y [y] z [z] | size [label size] | color [FF0000] | background [FFFFFF] | Show the distance between two atoms with a dashed line between the atoms and a label with the specified position, text, size, color, and background color |
| Analysis > Distance > between Two Sets | dist | 6ENY_B 6ENY_C | Show the distance between two sets with a dashed line between the center of masses and a label with the distance |
| Analysis > Distance > among Many Sets | disttable | [1st comma-separated sets] [2nd comma-separated sets] | Show the distances among many set in a table |
| Analysis > Distance > Hide | set lines off | Hide all distance lines and labels |
| Analysis > Surface Area | area | Calculate the solvent accessible surface area (SASA) for each residue in the current selection and show the result in a popup window |
| Analysis > Label > by Picking Atoms | N/A | Add a label to the center of two picked atoms in the 3D viewer |
| Analysis > Label > per Selection | select sets 6ENY_B; add label [my text] | x 125.6 y 98.76 z 87.23 | size 18 | color #ffff00 | background undefined | type custom | Add a custom label to the center of the current selection with the specified text, size, color, and background color |
| Analysis > Label > per Atom | add atom labels | Add labels of atom name for each atom in the current selection |
| Analysis > Label > per Atom Element | add element labels | Add labels of atom elements for each atom in the current selection |
| Analysis > Label > per Residue | add residue labels | Show one-letter residue labels for the current selection |
| Analysis > Label > per Residue & Number | add residue number labels | Show labels for residues in the current selection with the one-letter residue name followed by the residue number, e.g., R273 |
| Analysis > Label > N- & C- Termini | add terminal labels | Show labels for the N- and C- termini of each chain in the current selection |
| Analysis > Label > Change Label Color | set label color ffff00 | Change the color of all labels to the specified color (e.g., yellow with hex color code ffff00) |
| Analysis > Label > Remove | set labels off | Remove all labels |
| Analysis > Label Scale | set label scale [scale value] | Set the scale of all labels to the specified scale value (e.g., 2.0) |
| Analysis > Chem. Binding > Show | set chemicalbinding show | Show the chemical binding interactions in 3D |
| Analysis > Chem. Binding > Hide | set chemicalbinding hide | Remove the chemical binding interactions from 3D |
| Analysis > Assembly > Biological Assembly | set assembly on | Show the biological assembly for the current structure based on the assembly information provided in the PDB or mmCIF file |
| Analysis > Assembly > Asymmetric Unit | set assembly off | Show the asymmetric unit for the current structure based on the assembly information provided in the PDB or mmCIF file |
| Analysis > Symmetry > from PDB(precalculated) | symmetry C3 (global) | Show the symmetry (a prism and its central axis) for the current structure based on the symmetry information provided in the PDB or mmCIF file. The point group (e.g., C3) and scope (global or local) need to be specified. |
| Analysis > Symmetry > from SymD(Dynamic) | symd symmetry | Show the symmetry (a prism and its central axis) for the current structure based on the symmetry information calculated by SymD (http://symd.nci.nih.gov/). The alignment used in SymD is also shown. |
| Analysis > Symmetry > Show Axes Only | show axis | Show only the symmetry axes without the prisms |
| Analysis > Ref. Number > Show Ig for Selection | ig refnum on | Identify Ig domains and show the reference numbering for the identified Ig domains in the current selection based on the IgStrand numbering scheme for Ig domains (https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1012813) |
| Analysis > Window Title | your note | 2POR(MMDB) in iCn3D | Set the title of the iCn3D window to a custom text (e.g., "2POR(MMDB) in iCn3D") |
 |
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. 2020 Jan 1;36(1):131-135. (Epub 2019 June 20.) doi: 10.1093/bioinformatics/btz502. [PubMed PMID: 31218344] [Full Text at Oxford Academic] |  |
||
|
Wang J, Youkharibache P, Marchler-Bauer A, Lanczycki C, Zhang D, Lu S, Madej T, Marchler GH, Cheng T, Chong LC, Zhao S, Yang K, Lin J, Cheng Z, Dunn R, Malkaram SA, Tai C-H, Enoma D, Busby B, Johnson NL, Tabaro F, Song G, Ge Y. iCn3D: From Web-Based 3D Viewer to Structural Analysis Tool in Batch Mode. Front. Mol. Biosci. 2022 9:831740. (Epub 2022 Feb 17.) doi: 10.3389/fmolb.2022.831740. [PubMed PMID: 35252351] [Full Text at Frontiers] |
To embed iCn3D Structure Viewer in your own HTML page using iframe, simply add the following to your page. Note the URL should be the original URL with commands, not the shorten share link. The URL parameters are described at icn3d.html#parameters.
<iframe allow='xr-spatial-tracking *' allowFullScreen='true' src='https://www.ncbi.nlm.nih.gov/Structure/icn3d/?mmdbid=1tup&width=300&height=300&closepopup=1&showcommand=0&shownote=0&mobilemenu=1&showtitle=0' width='320' height='320' style='border:none'></iframe>To embed iCn3D Structure Viewer in your own HTML page using the distribution files on NCBI servers, simply follow these 3 steps. Note the changes to iCn3D version 3 are colored in red. (To embed multiple iCn3D viewers, see the source code of the example page for reference)
<link rel="stylesheet" href="https://www.ncbi.nlm.nih.gov/Structure/icn3d/lib/jquery-ui.min.css"> <link rel="stylesheet" href="https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.css"> <script src="https://www.ncbi.nlm.nih.gov/Structure/icn3d/lib/jquery.min.js"></script> <script src="https://www.ncbi.nlm.nih.gov/Structure/icn3d/lib/jquery-ui.min.js"></script> <script src="https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.min.js"></script>
<div id="icn3dwrap"></div>
The widget will be rendered inside of the div. <script type="text/javascript">
$( document ).ready(async function() {
var cfg = {
divid: 'icn3dwrap',
width: '100%',
height: '100%',
resize: true,
rotate: 'right',
mobilemenu: true,
showcommand: false,
showtitle: false
};
cfg['mmdbid'] = '1tup';
var icn3dui = new icn3d.iCn3DUI(cfg);
//communicate with the 3D viewer with chained functions
await icn3dui.show3DStructure();
// icn3dui.icn3d.setOptionCls.setOption('color', 'cyan');
// icn3dui.icn3d.setStyleCls.setBackground('transparent');
});
</script>
var atomDetails = {
serial: serial, // required, unique atom id
structure: structure, // required, used to identify the structure
chain: chain, // required, used to identify the chain
resi: resi, // required, used to identify residue ID, has to be a integer
name: atom, // required, atom name
coord: coord, // required, used to draw 3D shape
coord2: ribbonCoord, // optional, ribbon's real positions, used to draw stabilizers for 3D printing
bonds: [], // required, used to connect atoms
color: color, // optional, used to assign atom color, default is grey
style: style, // optional, used to assign atom style as one of 13 styles: ribbon, strand, cylinder and plate,
// nucleotide cartoon, o3' trace, schematic, c alpha trace, b factor tube, lines, stick,
// ball and stick, sphere, dot, nothing
style2: sideChainStyle, // optional, used to assign protein side chain style as one of 13 styles: ribbon, strand, cylinder and plate,
// nucleotide cartoon, o3' trace, schematic, c alpha trace, b factor tube, lines, stick,
// ball and stick, sphere, dot, nothing
het: false, // optional, used to determine chemicals, water, ions, etc
resn: resn, // optional, used to determine protein or nucleotide
b: b, // optional, used to draw B-factor tube
elem: elem, // optional, used to determine hydrogen bond
ss: 'coil', // optional, used to show secondary structures
ssbegin: false, // optional, used to show the beginning of secondary structures
ssend: false // optional, used to show the end of secondary structures
}
atoms: {}; // REQUIRED, all atoms in the input: atom index => atom details, ONLY THIS HASH STORE ALL ATOM DETAILS
dAtoms: {}; // REQUIRED, atoms used to display: atom index => 1
pmin: pmin; // REQUIRED, the position with minimum x,y,z
pmax: pmax; // REQUIRED, the position with maximum x,y,z
cnt: cnt; // REQUIRED, total number of atoms
maxD: pmax.distanceTo(pmin); // REQUIRED, max dimension of the structure
center: psum.multiplyScalar(1.0 / cnt); // REQUIRED, center position of the structure
hAtoms: {}; // OPTIONAL, atoms used to highlight: atom index => 1
structures: {}; // OPTIONAL, structure name => array of chain IDs
chains: {}; // OPTIONAL, structure_chain name => (atom index => 1)
residues: {}; // OPTIONAL, structure_chain_resi name => (atom index => 1)
chainsSeq: {}; // OPTIONAL, structure_chain name => array of residue object: {"name":[residue name], "resi": [residue number]}
chainsAn: {}; // OPTIONAL, structure_chain name => array of annotation
chainsAnTitle: []; // OPTIONAL, the titles for the array of annotation
molTitle: ""; // OPTIONAL, ID and name
hbondpnts: []; // OPTIONAL, array of positions of hydrogen bond
ssbondpnts: {}; // OPTIONAL, structure name => positions of disulfide bonds
residueId2Name: {}; // OPTIONAL, structure_chain_resi => one letter abbreviation
proteins: {}; // OPTIONAL, proteins: atom index => 1
sidec: {}; // OPTIONAL, protein sidechains: atom index => 1
calphas: {}; // OPTIONAL, protein C alphas: atom index => 1
nucleotides: {}; // OPTIONAL, DNA, RNA: atom index => 1
nucleotidesO3: {}; // OPTIONAL, DNA, RNA O3': atom index => 1
chemicals: {}; // OPTIONAL, chemicals: atom index => 1
ions: {}; // OPTIONAL, ions: atom index => 1
water: {}; // OPTIONAL, water: atom index => 1
| Global | Class (directory) | Class (directory) | Class (directory) | Functions |
|---|---|---|---|---|
| icn3d | icn3dui (src) | utilsCls (utils) | setIcn3d, setDialogAjax | |
| icn3d | icn3dui | utilsCls (utils) | isIE, isMobile, isMac, isSessionStorageSupported, hexToRgb, isCalphaPhosOnly, hasCovalentBond, residueName2Abbr, residueAbbr2Name, getJSONFromArray, checkFileAPI, getIdArray, compResid, toggle, setViewerWidthHeight | |
| icn3d | icn3dui | hashUtilsCls (utils) | cloneHash, intHash, exclHash, unionHash, unionHashInPlace, unionHashNotInPlace, intHash2Atoms, exclHash2Atoms, unionHash2Atoms, hash2Atoms, hashvalue2array | |
| icn3d | icn3dui | parasCls (utils) | Parameters: glycanHash, nucleotidesArray, ionsArray, cationsTrimArray, anionsTrimArray, ionCharges, vdwRadii, covalentRadii, surfaces, atomColors, defaultAtomColor, stdChainColors, backgroundColors, residueColors, residueArea, defaultResidueColor, chargeColors, hydrophobicColors, ssColors, ssColors2, b62ResArray, b62Matrix Functions: thr | |
| icn3d | icn3dui | myEventCls (utils) | onId, onIds | |
| icn3d | icn3dui | subdivideCls (utils) | subdivide, getKnot, getValueFromKnot | |
| icn3d | icn3dui | rmsdSuprCls (utils) | getRmsdSuprCls, eigen_values, null_basis, getEigenForSelection, getEigenVectors | |
| icn3d | icn3dui | convertTypeCls (utils) | passFloat32, passInt8, passInt16, passInt32, getUint8View, getDataView, getView, getBlobFromBufferAndText | |
| icn3d | icn3dui (src) | htmlCls (html) | N/A | |
| icn3d | icn3dui | htmlCls | alignSeqCls (html) | getAlignSequencesAnnotations |
| icn3d | icn3dui | htmlCls | clickMenuCls (html) | clickMenu1, clickMenu2, clickMenu3, clickMenu4, clickMenu5, clickMenu6, setLogCmd |
| icn3d | icn3dui | htmlCls | dialogCls (html) | openDlg, addSaveButton, addHideButton, getDialogStatus, openDlgHalfWindow, openDlg2Ddgm, openDlgRegular, openDlgNotebook |
| icn3d | icn3dui | htmlCls | eventsCls (html) | fullScreenChange, allEventFunctions |
| icn3d | icn3dui | htmlCls | setDialogCls (html) | setCustomDialogs, setDialogs |
| icn3d | icn3dui | htmlCls | setHtmlCls (html) | getLink, getLinkWrapper, getRadio, getRadioColor, setAdvanced, getOptionHtml, setColorHints, setThicknessHtml, setSequenceGuide, setAlignSequenceGuide, getSelectionHints, addGsizeSalt, getFootHtml, getPotentialHtml, exportPqr, clickReload_pngimage, setLineThickness, updateSurfPara, exportPdb |
| icn3d | icn3dui | htmlCls | setMenuCls (html) | setTopMenusHtml, setTopMenusHtmlMobile, setReplayHtml, setTools, setButton, setTools_base, setTheme, setLogWindow, setMenu1, setMenu1_base, setMenu2, setMenu2_base, setMenu2b, setMenu2b_base, setMenu3, setMenu3_base, setMenu4, setMenu4_base, setMenu5, setMenu5_base, setMenu6, setMenu6_base, hideMenu, showMenu |
| icn3d | icn3dui (src) | icn3d (icn3d) | init, init_base, reinitAfterLoad, resetConfig | |
| icn3d | icn3dui | icn3d | analysisCls (analysis) | calculateArea, calcBuriedSurface, measureDistTwoSets, addLine, addLineFromPicking, addLabel, addChainLabels, addTerminiLabels |
| icn3d | icn3dui | icn3d | applySymdCls (analysis) | applySymd, applySymmetry |
| icn3d | icn3dui | icn3d | delphiCls (analysis) | CalcPhiUrl, CalcPhi, PhiParser, loadPhiData, loadCubeData, applyCommandPhi, applyCommandDelphi, loadDelphiFile, loadPhiFile, loadPhiFileUrl |
| icn3d | icn3dui | icn3d | diagram2dCls (analysis) | draw2Ddgm, set2DdgmNote, highlightNode, removeLineGraphSelection, removeScatterplotSelection, click2Ddgm, selectInteraction, selectInteractionAtoms, draw2DProtein, draw2DNucleotide, draw2DChemical |
| icn3d | icn3dui | icn3d | cartoon2dCls (analysis) | draw2Dcartoon, click2Dcartoon |
| icn3d | icn3dui | icn3d | dsspCls (analysis) | applyDssp, parseDsspData |
| icn3d | icn3dui | icn3d | scapCls (analysis) | applyCommandScap, adjust2DWidth, retrieveScap |
| icn3d | icn3dui | icn3d | symdCls (analysis) | applyCommandSymd, retrieveSymd, getResObj, setSeqAlignForSymmetry, retrieveSymmetry, getPolygonColor, getAxisColor |
| icn3d | icn3dui | icn3d | addTrackCls (annotations) | clickAddTrackButton, showNewTrack, alignSequenceToStructure, defineSecondary, simplifyText, checkGiSeq, getFullText, setCustomFile |
| icn3d | icn3dui | icn3d | annoCddSiteCls (annotations) | showCddSiteAll, setDomainFeature, showAnnoType, setToolTip |
| icn3d | icn3dui | icn3d | annoContactCls (annotations) | showInteraction, showInteraction_base |
| icn3d | icn3dui | icn3d | annoPTMCls (annotations) | showPTM |
| icn3d | icn3dui | icn3d | annoCrossLinkCls (annotations) | showCrosslink, showCrosslink_base |
| icn3d | icn3dui | icn3d | annoDomainCls (annotations) | showDomainPerStructure, showDomainAll, showDomainWithData |
| icn3d | icn3dui | icn3d | annoSnpClinVarCls (annotations) | navClinVar, showClinVarLabelOn3D, getSnpLine, processSnpClinvar, showClinvarPart2, showSnp, showClinvar, showSnpClinvar, showSnpPart2, processNoClinvar, processNoSnp |
| icn3d | icn3dui | icn3d | annoSsbondCls (annotations) | showSsbond, showSsbond_base |
| icn3d | icn3dui | icn3d | annoTransMemCls (annotations) | showTransmem, showTransmem_base |
| icn3d | icn3dui | icn3d | annotationCls (annotations) | hideAllAnno, hideAllAnnoBase, setAnnoSeqBase, setAnnoTabBase, setAnnoTabAll, hideAnnoTabAll, resetAnnoAll, resetAnnoTabAll, setAnnoTabCustom, hideAnnoTabCustom, setAnnoTabClinvar, hideAnnoTabClinvar, setAnnoTabSnp, hideAnnoTabSnp, setAnnoTabCdd, hideAnnoTabCdd, setAnnoTab3ddomain, hideAnnoTab3ddomain, setAnnoTabSite, hideAnnoTabSite, setAnnoTabInteraction, hideAnnoTabInteraction, setAnnoTabSsbond, hideAnnoTabSsbond, setAnnoTabCrosslink, hideAnnoTabCrosslink, setAnnoTabTransmem, hideAnnoTabTransmem, setTabs, clickCdd, showAnnoSelectedChains, showAnnoAllChains, setAnnoView, setAnnoDisplay, showFixedTitle, hideFixedTitle, setAnnoViewAndDisplay, updateClinvar, updateSnp, updateDomain, updateInteraction, updatPTM, updateSsbond, updateCrosslink, updateTransmem |
| icn3d | icn3dui | icn3d | showAnnoCls (annotations) | showAnnotations, showAnnoSeqData, getAnnotationData, getSequenceData, getCombinedSequenceData, processSeqData, enableHlSeq, getAnDiv, addButton, addSnpButton, conservativeReplacement, getColorhexFromBlosum62 |
| icn3d | icn3dui | icn3d | showSeqCls (annotations) | showSeq, insertGap, insertGapOverview, setAlternativeSeq, getProteinName |
| icn3d | icn3dui | icn3d | alternateCls (display) | alternateStructures, alternateWrapper |
| icn3d | icn3dui | icn3d | applyCenterCls (display) | applyCenterOptions, setRotationCenter, setCenter, centerSelection, centerAtoms, setWidthHeight |
| icn3d | icn3dui | icn3d | applyClbondsCls (display) | applyClbondsOptions, applyClbondsOptions_base |
| icn3d | icn3dui | icn3d | applyDisplayCls (display) | applyDisplayOptions, selectMainChainSubset |
| icn3d | icn3dui | icn3d | applyOtherCls (display) | applyOtherOptions, applyChemicalbindingOptions, updateStabilizer, getResidueRepPos |
| icn3d | icn3dui | icn3d | applySsbondsCls (display) | applySsbondsOptions |
| icn3d | icn3dui | icn3d | cameraCls (display) | setCamera |
| icn3d | icn3dui | icn3d | drawCls (display) | draw, applyTransformation, render |
| icn3d | icn3dui | icn3d | fogCls (display) | setFog |
| icn3d | icn3dui | icn3d | sceneCls (display) | rebuildScene, rebuildSceneBase |
| icn3d | icn3dui | icn3d | setColorCls (display) | setColorByOptions, setAtmClr, updateChainsColor, setMmdbChainColor, setConservationColor, applyOriginalColor, applyPrevColor, setOutlineColor |
| icn3d | icn3dui | icn3d | setOptionCls (display) | setOption, setStyle, saveStyle, applySavedStyle, saveColor, applySavedColor |
| icn3d | icn3dui | icn3d | setStyleCls (display) | setStyle2Atoms, setAtomStyleByOptions, setBackground, saveCommandsToSession, getCommandsBeforeCrash, handleContextLost, adjustIcon |
| icn3d | icn3dui | icn3d | export3DCls (export) | exportStlFile, exportVrmlFile, getFaceCnt, saveStlFile, updateArray, processStlMeshGroup, saveVrmlFile, processVrmlMeshGroup |
| icn3d | icn3dui | icn3d | saveFileCls (export) | saveFile, saveSvg, getSvgXml, savePng, exportCustomAtoms, getAtomPDB, getSelectedResiduePDB, getPDBHeader, showTitle, getLinkToStructureSummary, setEntrezLinks |
| icn3d | icn3dui | icn3d | shareLinkCls (export) | shareLink, shareLinkUrl, getPngText |
| icn3d | icn3dui | icn3d | threeDPrintCls (export) | setThichknessFor3Dprint, prepareFor3Dprint, resetAfter3Dprint, removeOneStabilizer, outputSelection, addStabilizer, hideStabilizer, getResidueRepAtom |
| icn3d | icn3dui | icn3d | axesCls (geometry) | buildAxes, buildAllAxes, createArrow, setPc1Axes |
| icn3d | icn3dui | icn3d | boxCls (geometry) | createBox, createBox_base, createBoxRepresentation_P_CA |
| icn3d | icn3dui | icn3d | brickCls (geometry) | createBrick |
| icn3d | icn3dui | icn3d | cartoonNuclCls (geometry) | drawStrandNucleicAcid, drawNucleicAcidStick |
| icn3d | icn3dui | icn3d | curveCls (geometry) | createCurveSub |
| icn3d | icn3dui | icn3d | curveStripArrowCls (geometry) | createCurveSubArrow, createStripArrow, prepareStrand |
| icn3d | icn3dui | icn3d | cylinderCls (geometry) | createCylinder, createCylinder_base, createCylinderHelix, createCylinderCurve |
| icn3d | icn3dui | icn3d | glycanCls (geometry) | showGlycans |
| icn3d | icn3dui | icn3d | impostorCls (geometry) | setParametersForShader , drawImpostorShader , getShader , createImpostorShaderBase, createImpostorShaderCylinder, createImpostorShaderSphere, clearImpostors |
| icn3d | icn3dui | icn3d | instancingCls (geometry) | positionFromGeometry, colorFromGeometry, indexFromGeometry, normalFromGeometry, drawSymmetryMates, applyMat, drawSymmetryMatesNoInstancing, createInstancedGeometry, getInstancedMaterial, createInstancedMesh, drawSymmetryMatesInstancing |
| icn3d | icn3dui | icn3d | labelCls (geometry) | makeTextSprite, createLabelRepresentation, hideLabels |
| icn3d | icn3dui | icn3d | lineCls (geometry) | createLineRepresentation, createConnCalphSidechain, createSingleLine, createLines |
| icn3d | icn3dui | icn3d | reprSubCls (geometry) | createRepresentationSub |
| icn3d | icn3dui | icn3d | residueLabelsCls (geometry) | addResidueLabels, addNonCarbonAtomLabels, addAtomLabels |
| icn3d | icn3dui | icn3d | sphereCls (geometry) | createSphere, createSphereBase, createSphereRepresentation |
| icn3d | icn3dui | icn3d | stickCls (geometry) | createStickRepresentation |
| icn3d | icn3dui | icn3d | strandCls (geometry) | createStrand, getOneExtraResidue |
| icn3d | icn3dui | icn3d | stripCls (geometry) | createStrip, setCalphaDrawnCoord |
| icn3d | icn3dui | icn3d | tubeCls (geometry) | createTube, getCustomtubesize, createTubeSub, getRadius |
| icn3d | icn3dui | icn3d | hlObjectsCls (highlight) | addHlObjects, removeHlObjects |
| icn3d | icn3dui | icn3d | hlSeqCls (highlight) | selectSequenceNonMobile, selectSequenceMobile, selectChainMobile, selectTitle, selectResidues |
| icn3d | icn3dui | icn3d | hlUpdateCls (highlight) | update2DdgmContent, changeSeqColor, removeHlAll, removeHlObjects, removeHlSeq, removeHl2D, removeHlMenus, updateHlAll, updateHlObjects, updateHlSeq, updateHlSeqInChain, updateHl2D, updateHlMenus, hlSequence, hlSeqInChain, toggleHighlight, clearHighlight, showHighlight, highlightChains, hlSummaryDomain3ddomain, updateHlAll |
| icn3d | icn3dui | icn3d | contactCls (interaction) | getAtomsWithinAtom, getNeighboringAtoms, getExtent, hideContact |
| icn3d | icn3dui | icn3d | drawGraphCls (interaction) | drawGraph |
| icn3d | icn3dui | icn3d | getGraphCls (interaction) | getGraphData, drawResNode, getNodeTopBottom, updateGraphJson, updateGraphColor, handleForce, getNodesLinksForSet, getHbondLinksForSet, getIonicLinksForSet, getHalogenPiLinksForSet, getContactLinksForSet, getContactLinks, compNode, getGraphLinks, convertLabel2Resid |
| icn3d | icn3dui | icn3d | hBondCls (interaction) | isHbondDonorAcceptor, calcAngles, calcPlaneAngle, isValidHbond, calculateChemicalHbonds, setHbondsContacts, hideHbonds |
| icn3d | icn3dui | icn3d | lineGraphCls (interaction) | drawLineGraph, drawLineGraph_base, drawScatterplot_base, copyStylesInline |
| icn3d | icn3dui | icn3d | piHalogenCls (interaction) | calculateHalogenPiInteractions, getHalogenDonar, getHalogenAcceptor, getPi, getCation, getHalogenPiInteractions, getRingNormal, getAromaticRings, dfs_cycle, getAromaticPisLigand, hideHalogenPi |
| icn3d | icn3dui | icn3d | saltbridgeCls (interaction) | calculateIonicInteractions, hideSaltbridge |
| icn3d | icn3dui | icn3d | showInterCls (interaction) | showInteractions, showHbonds, showHydrogens, hideHydrogens, hideHbondsContacts, showIonicInteractions, showHalogenPi, showClbonds, showSsbonds, pickCustomSphere, pickCustomSphere_base |
| icn3d | icn3dui | icn3d | viewInterPairsCls (interaction) | viewInteractionPairs, clearInteractions, resetInteractionPairs, retrieveInteractionData, getAllInteractionTable, getInteractionPerResidue, getInteractionPairDetails, getContactPairDetails, exportInteractions, exportSsbondPairs, exportClbondPairs, exportHbondPairs, exportSaltbridgePairs, exportHalogenPiPairs, exportSpherePairs |
| icn3d | icn3dui | icn3d | alignParserCls (parsers) | downloadAlignment, downloadAlignmentPart2, loadOpmDataForAlign |
| icn3d | icn3dui | icn3d | chainalignParserCls (parsers) | downloadChainalignmentPart2, downloadChainalignmentPart3, downloadChainalignment, parseChainAlignData, loadOpmDataForChainalign |
| icn3d | icn3dui | icn3d | densityCifParserCls (parsers) | densityCifParser, parseChannels, getChannel, CIFParse, BinaryParse, MessagePackParse |
| icn3d | icn3dui | icn3d | dsn6ParserCls (parsers) | dsn6Parser, dsn6ParserBase, loadDsn6Data, getMatrix, loadDsn6File, loadDsn6FileUrl |
| icn3d | icn3dui | icn3d | loadAtomDataCls (parsers) | loadAtomDataIn |
| icn3d | icn3dui | icn3d | loadPDBCls (parsers) | loadPDB, adjustSeq, setSsbond, getChainCalpha |
| icn3d | icn3dui | icn3d | mmcifParserCls (parsers) | downloadMmcif, downloadMmcifSymmetry, loadMmcifData |
| icn3d | icn3dui | icn3d | mmdbParserCls (parsers) | parseMmdbData, downloadMmdb, downloadBlast_rep_id, loadMmdbOpmData |
| icn3d | icn3dui | icn3d | bcifParserCls (parsers) | downloadBcif, parseBcifData |
| icn3d | icn3dui | icn3d | mol2ParserCls (parsers) | loadMol2Data, loadMol2AtomData |
| icn3d | icn3dui | icn3d | opmParserCls (parsers) | downloadOpm, loadOpmData, setOpmData, parseAtomData |
| icn3d | icn3dui | icn3d | ParserUtilsCls (parsers) | alignCoords, getMissingResidues, set2DDiagramsForAlign, set2DDiagramsForChainalign, parse2DDiagramsData, set2DDiagrams, showLoading, hideLoading, setYourNote, transformToOpmOri, transformToOpmOriForAlign, addOneDumAtom, addMemAtoms, setMaxD, renderStructure |
| icn3d | icn3dui | icn3d | pdbParserCls (parsers) | downloadPdb, downloadUrl, loadPdbData, loadPdbDataRender |
| icn3d | icn3dui | icn3d | realignParserCls (parsers) | realign, parseChainRealignData, realignOnSeqAlign, realignChainOnSeqAlign |
| icn3d | icn3dui | icn3d | sdfParserCls (parsers) | downloadCid, loadSdfData, loadSdfAtomData |
| icn3d | icn3dui | icn3d | setSeqAlignCls (parsers) | setSeqAlign, setSeqAlignChain, setSeqAlignForRealign, setSeqPerResi |
| icn3d | icn3dui | icn3d | xyzParserCls (parsers) | loadXyzData, setXyzAtomSeq, loadXyzAtomData |
| icn3d | icn3dui | icn3d | dcdParserCls (parsers) | loadDcdData |
| icn3d | icn3dui | icn3d | xtcParserCls (parsers) | loadXtcData |
| icn3d | icn3dui | icn3d | controlCls (picking) | setControl, mouseMove |
| icn3d | icn3dui | icn3d | pickingCls (picking) | showPicking, showPickingBase, showPickingHilight, select3ddomainFromAtom, selectStrandHelixFromAtom |
| icn3d | icn3dui | icn3d | rayCls (picking) | rayCasterBase, isIntersect, getAtomsFromPosition |
| icn3d | icn3dui | icn3d | applyCommandCls (selection) | applyCommand, setStrengthPara, getThresholdNameArrays, setQueryresi2score, getMenuFromCmd |
| icn3d | icn3dui | icn3d | definedSetsCls (selection) | setProtNuclLigInMenu, setPredefinedInMenu, setAtomMenu, setChainsInMenu, setTransmemInMenu, showSets, clickCustomAtoms, deleteSelectedSets, changeCustomAtoms, setHAtomsFromSets, updateAdvancedCommands, combineSets, commandSelect, clickCommand_apply, selectCombinedSets, clickModeswitch, setModeAndDisplay, setMode, getAtomsFromOneSet, getAtomsFromSets, getAtomsFromNameArray |
| icn3d | icn3dui | icn3d | firstAtomObjCls (selection) | getFirstAtomObj, getFirstCalphaAtomObj, getFirstAtomObjByName, getLastAtomObj, getResiduesFromAtoms, getResiduesFromCalphaAtoms, getChainsFromAtoms, getAtomFromResi, getAtomCoordFromResi |
| icn3d | icn3dui | icn3d | loadScriptCls (selection) | loadScript, execCommands, execCommandsBase, pressCommandtext, applyCommandLoad, applyCommandMap, applyCommandEmmap, applyCommandRealign, applyCommandGraphinteractionBase, applyCommandGraphinteraction, applyCommandAnnotationsAndCddSite, applyCommandClinvarBase, applyCommandSnpBase, applyCommandClinvar, applyCommandSnp, applyCommand3ddomainBase, applyCommand3ddomain, applyCommandViewinteractionBase, applyCommandViewinteraction, renderFinalStep, replayFirstStep |
| icn3d | icn3dui | icn3d | resid2specCls (selection) | residueids2spec, atoms2spec, atoms2residues, selectProperty, selectComplement, switchHighlightLevel, switchHighlightLevelUp, switchHighlightLevelDown |
| icn3d | icn3dui | icn3d | selectByCommandCls (selection) | selectByCommand, selectBySpec |
| icn3d | icn3dui | icn3d | selectionCls (selection) | selectAll, selectAll_base, selectAChain, selectResidueList, selectMainChains, selectSideChains, selectMainSideChains, clickShow_selected, clickHide_selected, getGraphDataForDisplayed, updateSelectionNameDesc, addCustomSelection, showSelection, hideSelection, saveSelection, removeSelection, resetAll, loadSelection, oneStructurePerWindow, showAll, saveSelectionIfSelected, saveSelectionPrep, selectOneResid, toggleSelection, toggleMembrane, adjustMembrane, selectBtwPlanes |
| icn3d | icn3dui | icn3d | applyMapCls (surface) | applySurfaceOptions, applyMapOptions, applyEmmapOptions, applyPhimapOptions, applyphisurfaceOptions, removeSurfaces, removeLastSurface, removeMaps, removeEmmaps, removePhimaps, removeLastMap, removeLastEmmap, removeLastPhimap |
| icn3d | icn3dui | icn3d | electronMapCls (surface) | getFacesAndVertices, initparm, transformMemPro, fillvoxels, buildboundary, marchingcubeinit, counter, marchingcube |
| icn3d | icn3dui | icn3d | marchingCubeCls (surface) | march, laplacianSmooth |
| icn3d | icn3dui | icn3d | proteinSurfaceCls (surface) | getVDWIndex, inOrigExtent, getFacesAndVertices, initparm, boundingatom, fillvoxels, fillAtom, fillvoxelswaals, fillAtomWaals, buildboundary, fastdistancemap, fastoneshell, marchingcubeinit, counter, marchingcube |
| icn3d | icn3dui | icn3d | surfaceCls (surface) | createSurfaceRepresentation, transformMemPro, SetupSurface, SetupMap |
| icn3d | icn3dui | icn3d | resizeCanvasCls (transform) | resizeCanvas, windowResize, openFullscreen, rotStruc, back, forward, replayon, replayoff, closeDialogs |
| icn3d | icn3dui | icn3d | transformCls (transform) | resetOrientation, rotateLeft , rotateRight , rotateUp , rotateDown , rotate_base , setRotation, translateLeft, translateRight, translateUp, translateDown, translate_base, zoomIn, zoomOut, zoominSelection, getTransformationStr |
var loadStateFileCls = new LoadStateFile(icn3dui.icn3d);
loadStateFileCls.loadStateFile('color spectrum');
// import any classes from icn3d.module.js to be used in your class
import {LoadScript} from './icn3d.module.js';
// class name starts with a upper-case letter
class LoadStateFile {
// pass the instance of the class iCn3D
constructor(icn3d) {
this.icn3d = icn3d;
}
// functions start with a lower-case letter
// use "ic" to access the instance of iCn3D class
loadStateFile(fileStr) { var ic = this.icn3d;
// "ic" has a lot of class instances such as "loadScriptCls"
ic.loadScriptCls.loadScript(fileStr, true);
}
}
// export your class
export {LoadStateFile}
icn3d.Picking.prototype.showPicking = function(atom, x, y) { var ic = this.icn3d, me = ic.icn3dui;
// 1. copy the function showPicking() here
// 2. Modify the function as if it is in the class "Picking"
}