Dynamically generated for selected residues. Nodes can be dragged or clicked.
Label:
Selection: Name:
Select on 1D sequences: drag to select, drag again to deselect, multiple selection is allowed without Ctrl key, click "Save Selection" to save the current selection.
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.
Select on 3D structures: hold "Alt" and use mouse to pick, click the second time to deselect, 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" to save the current selection.
Save the current selection(either on 3D structure, 2D interactions, or 1D sequence): open the menu "Select -> Save Selection", specify the name and description for the selection, and click "Save".
Residue labeling: aligned residue with coordinates: UPPER case letter; non-aligned residue with coordinates: lower case letter which can be highlighted; residue missing coordinates: lower case letter which can NOT be highlighted.
Defined Sets: Set Operations:
Select:
Name:
Specification Tips:
Specification: In the selection "$1HHO,4N7N.A,B,C:5-10,LV,3AlaVal,chemicals@CA,C":
"$1HHO,4N7N" uses "$" to indicate structure selection.
".A,B,C" uses "." to indicate chain selection.
":5-10,LV,3LeuVal,chemicals" uses the colon ":" to indicate residue selection. Residue selection could be residue number(5-10), one-letter IUPAC residue name abbreviations(LV), three-letter residue names(AlaVal, "3" indicates each residue name has three letters), or predefined names: "proteins", "nucleotides", "chemicals", "ions", and "water". IUPAC abbreviations can be written either as a contiguous string(e.g., ":LV"), in order to find all instances of that sequence in the structure, or they can be separated by commas(e.g., ":L,V") to select all residues of a given type in the structure(in the latter case, select all Leucine and Valine in the structure).
"@CA,C" uses "@" to indicate atom selection.
Partial definition is allowed, e.g., ":1-10" selects all residue IDs 1-10 in all chains.
Different selections can be unioned(with "or", default), intersected(with "and"), or negated(with "not"). For example, ":1-10 or :K" selects all residues 1-10 and all Lys residues. ":1-10 and :K" selects all Lys residues in the range of residue number 1-10. ":1-10 or not :K" selects all residues 1-10, which are not Lys residues.
The wild card character "X" or "x" can be used to represent any character.
Set Operation:
Users can select multiple sets in the menu "Select > Defined Sets".
Different sets can be unioned(with "or", default), intersected(with "and"), or negated(with "not"). For example, if the "Defined Sets" menu has four sets ":1-10", ":11-20", ":5-15", and ":7-8", the command "saved atoms :1-10 or :11-20 and :5-15 not :7-8" unions all residues 1-10 and 11-20 to get the residues 1-20, then intersects with the residues 5-15 to get the residues 5-15, then exclude the residues 7-8 to get the final residues 5-6 and 9-15.
Full commands in url or command window:
Select without saving the set: select $1HHO,4N7N.A,B,C:5-10,LV,chemicals@CA,C
Select and save: select $1HHO,4N7N.A,B,C:5-10,LV,chemicals@CA,C | name my_name
Select:
Name:
Specification Tips:
Specification: In the selection "$1HHO,4N7N.A,B,C:5-10,LV,3AlaVal,chemicals@CA,C":
"$1HHO,4N7N" uses "$" to indicate structure selection.
".A,B,C" uses "." to indicate chain selection.
":5-10,LV,3LeuVal,chemicals" uses the colon ":" to indicate residue selection. Residue selection could be residue number(5-10), one-letter IUPAC residue name abbreviations(LV), three-letter residue names(AlaVal, "3" indicates each residue name has three letters), or predefined names: "proteins", "nucleotides", "chemicals", "ions", and "water". IUPAC abbreviations can be written either as a contiguous string(e.g., ":LV"), in order to find all instances of that sequence in the structure, or they can be separated by commas(e.g., ":L,V") to select all residues of a given type in the structure(in the latter case, select all Leucine and Valine in the structure).
"@CA,C" uses "@" to indicate atom selection.
Partial definition is allowed, e.g., ":1-10" selects all residue IDs 1-10 in all chains.
Different selections can be unioned(with "or", default), intersected(with "and"), or negated(with "not"). For example, ":1-10 or :K" selects all residues 1-10 and all Lys residues. ":1-10 and :K" selects all Lys residues in the range of residue number 1-10. ":1-10 or not :K" selects all residues 1-10, which are not Lys residues.
The wild card character "X" or "x" can be used to represent any character.
Set Operation:
Users can select multiple sets in the menu "Select > Defined Sets".
Different sets can be unioned(with "or", default), intersected(with "and"), or negated(with "not"). For example, if the "Defined Sets" menu has four sets ":1-10", ":11-20", ":5-15", and ":7-8", the command "saved atoms :1-10 or :11-20 and :5-15 not :7-8" unions all residues 1-10 and 11-20 to get the residues 1-20, then intersects with the residues 5-15 to get the residues 5-15, then exclude the residues 7-8 to get the final residues 5-6 and 9-15.
Full commands in url or command window:
Select without saving the set: select $1HHO,4N7N.A,B,C:5-10,LV,chemicals@CA,C
Select and save: select $1HHO,4N7N.A,B,C:5-10,LV,chemicals@CA,C | name my_name
Note: VAST+ finds other macromolecular structures that have a similar biological unit. To do this, VAST+ takes into consideration the complete set of 3D domains that VAST identified within a query structure, throughout all of its component protein molecules, and finds other macromolecular structures that have a similar set of proteins/3D domains.
PDB ID:
Note: VAST identifies 3D domains (substructures) within each protein structure in the Molecular Modeling Database (MMDB), and then finds other protein structures that have one or more similar 3D domains, using purely geometric criteria. You have two ways to do a VAST search.
Optione 1, search with your selection (all residues are selected by default) in the loaded structures:
Optione 2, search with PDB ID and chain name: PDB ID: Chain Name:
Optione 3, search with a PDB file:
1. your selection (all residues are selected by default) in the loaded structures to Foldseek web server.
2 (Optional). Once you see the structure neighbors, you can view the alignment in iCn3D by inputing a list of PDB chain IDs or AlphaFold UniProt IDs below.
The PDB chain IDs are the same as the record names such as "1hho_A". The UniProt ID is the text between "AF-" and "-F1". For example, the UniProt ID for the record name "AF-P69905-F1-model_v4" is "P69905".
Chain ID List:
MMTF ID:
PDB ID:
Note: AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100:
Very high (pLDDT > 90) Confident (90 > pLDDT > 70) Low (70 > pLDDT > 50) Very low (pLDDT < 50)
Note: Several PDB files could be concatenated into a single PDB file. Use the line "ENDMDL" to separate PDB files.
PDB File:
Multiple PDB Files:
The custom JSON file on residue colors has the following format for proteins("ALA" and "ARG") and nucleotides("G" and "A"): {"ALA":"#C8C8C8", "ARG":"#145AFF", ..., "G":"#008000", "A":"#6080FF", ...}
Residue Color File:
The custom file for the structure has two columns separated by space or tab: residue number, and score in the range of 0-100. If you click "Apply Custom Color" button, the scores 0, 50 and 100 correspond to the three colors specified below. If you click "Apply Custom Tube", the selected residues will be displayed in a style similar to "B-factor Tube".
Custom File:
1. Score to Color: 0:50: 100: or
2.
You can define your own reference numbers in a custom file using Excel, and then export it as a CSV file. An example file is shown below with cells separated by commas.
The first row defines the reference residue numbers. The 1st cell could be anything. The rest cells are reference residue numbers (e.g., 11, 12, 21, 22) or empty cells. Each chain has a separate row. The first cell of the second row is the chain ID "1TUP_A". The rest cells are the corresponding real residue numbers for reference residue numbers in the first row. For example, the reference numbers for residues 100, 101, and 132 in the chain 1TUP_A are 11, 12, and 22, respectively. The thrid row shows the real residue numbers for the chain "1TUP_B".
To select all residues corresponding to the reference numbers, you can simplay replace ":" with "%" in the Specification. For example, "%12" selects the residue 101 in 1TUP_A and the residue 111 in 1TUP_B. ".A%12" has the chain "A" filter and selects the residue 101 in 1TUP_A.
All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures).
Chain IDs:
(Note: To align chains in custom PDB files, you could load them in "File > Open File > PDB Files (appendable)" and click "Analysis > Defined Sets". Finally select multiple chains in Defined Sets and click "File > Realign Selection".)
All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures).
Chain IDs:
The sequence alignment (followed by structure alignemnt) is based on residue numbers in the First/Master chain:
(Note: To align chains in custom PDB files, you could load them in "File > Open File > PDB Files (appendable)" and click "Analysis > Defined Sets". Finally select multiple chains in Defined Sets and click "File > Realign Selection".)
All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures).
Chain IDs:
Each alignment is defined as " | "-separated residue lists in one line. "10-50" means a range of residues from 10 to 50.
Option 1:
Option 2:
All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures).
Chain IDs:
Each alignment is defined as " | "-separated residue lists in one line. "10-50" means a range of residues from 10 to 50.
Please specify the mutations with a comma separated mutation list. Each mutation can be specified as "[uppercase PDB ID or AlphaFold UniProt ID]_[Chain ID]_[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".
Mutations:
ID Type: PDB IDAlphaFold UniProt ID
Show Mutation in: Current PageNew Page
Mol2 File:
SDF File:
XYZ File:
AlphaFold PAE File:
File type: URL in the same host:
mmCIF File:
mmCIF ID:
MMDB or PDB ID:
Note: The "biological unit" is the biochemically active form of a biomolecule,
which can range from a monomer (single protein molecule) to an oligomer of 100+ protein molecules.
The "asymmetric unit" is the raw 3D structure data resolved by X-ray crystallography, NMR, or Cryo-electron microscopy. The asymmetric unit is equivalent to the biological unit in approximately 60% of structure records. In the remaining 40% of the records, the asymmetric unit represents a portion of the biological unit that can be reconstructed using crystallographic symmetry, or it represents multiple copies of the biological unit.
List of PDB, MMDB, or AlphaFold UniProt IDs:
Note: The "biological unit" is the biochemically active form of a biomolecule,
which can range from a monomer (single protein molecule) to an oligomer of 100+ protein molecules.
The "asymmetric unit" is the raw 3D structure data resolved by X-ray crystallography, NMR, or Cryo-electron microscopy. The asymmetric unit is equivalent to the biological unit in approximately 60% of structure records. In the remaining 40% of the records, the asymmetric unit represents a portion of the biological unit that can be reconstructed using crystallographic symmetry, or it represents multiple copies of the biological unit.
Enter a Sequence ID (or FASTA sequence) and the aligned Structure ID, which can be found using the BLAST search against the pdb database with the Sequence ID or FASTA sequence as input.
Sequence ID(NCBI protein accession of a sequence): or FASTA sequence:
Structure ID(NCBI protein accession of a chain of a 3D structure):
Your note will be saved in the HTML file when you click "File > Save File > iCn3D PNG Image".
Protein gi:
PubChem CID:
iCn3D PNG image:
State file:
Since January 6, 2021, you can show the original view with the archived version of iCn3D by pasting your URL below and click "Show Originial View". Note the version in the parameter "v" was used to replace "full.html" with "full_[v].html" in the URL.
Share Link URL:
Selection file:
Preference file:
Note: Always load a PDB file before loading DSN6 files.
2fofc contour at: σ
fofc contour at: σ
Note: Always load a PDB file before loading DSN6 files.
Note: Only the selected residues are used for DelPhi potential calculation by solving linear Poisson-Boltzmann equation.
The hydrogens and partial charges of proteins and nucleotides are added using DelPhiPKa with the Amber charge and size files. The hydrogens of ligands are added using Open Babel. The partial charges of ligands are calculated using Antechamber with the Gasteiger charge method. All partial charges are calculated at pH 7.
Lipids are treated as ligands. Please use "HETATM" instead of "ATOM " for each lipid atom in your PDB file. Each phosphate in lipids is assigned with a charge of -1. You can download PQR and modify it, or prepare your PQR file using other tools. Then load the PQR file at the menu "Analysis > Load PQR/Potential".
Grid Size: Salt Concentration: M
Surface with max potential at: kT/e(25.6mV at 298K)
Surface: Opacity: Wireframe:
Note: Only the selected residues are used for DelPhi potential calculation by solving linear Poisson-Boltzmann equation.
The hydrogens and partial charges of proteins and nucleotides are added using DelPhiPKa with the Amber charge and size files. The hydrogens of ligands are added using Open Babel. The partial charges of ligands are calculated using Antechamber with the Gasteiger charge method. All partial charges are calculated at pH 7.
Lipids are treated as ligands. Please use "HETATM" instead of "ATOM " for each lipid atom in your PDB file. Each phosphate in lipids is assigned with a charge of -1. You can download PQR and modify it, or prepare your PQR file using other tools. Then load the PQR file at the menu "Analysis > Load PQR/Potential".
Note: Always load a PDB file before loading a PQR or DelPhi potential file.
The PDB file can be loaded in the URL with "pdbid=" or at "File > Open File". The PQR file can be prepared at the menu "Analysis > Download PQR" with your modification or using other tools. The DelPhi potential file can be calculated at DelPhi Web Server and be exported as a Cube file.
Surface with max potential at: kT/e(25.6mV at 298K)
Note: Always load a PDB file before loading a PQR or DelPhi potential file.
The PDB file can be loaded in the URL with "pdbid=" or at "File > Open File". The PQR file can be prepared at the menu "Analysis > Download PQR" with your modification or using other tools. The DelPhi potential file can be calculated at DelPhi Web Server and be exported as a Cube file.
Note: Always load a PDB file before loading a PQR or DelPhi potential file.
The PDB file can be loaded in the URL with "pdbid=" or at "File > Open File". The PQR file can be prepared at the menu "Analysis > Download PQR" with your modification or using other tools. The DelPhi potential file can be calculated at DelPhi Web Server and be exported as a Cube file. The PQR or potential file can be accessed in a URL if it is located in the same host as iCn3D.
Surface with max potential at: kT/e(25.6mV at 298K)
Note: Always load a PDB file before loading a PQR or DelPhi potential file.
The PDB file can be loaded in the URL with "pdbid=" or at "File > Open File". The PQR file can be prepared at the menu "Analysis > Download PQR" with your modification or using other tools. The DelPhi potential file can be calculated at DelPhi Web Server and be exported as a Cube file. The PQR or potential file can be accessed in a URL if it is located in the same host as iCn3D.
Symmetry:
Distance: Contact Type:
1. Choose interaction types and their thresholds:
Hydrogen Bonds
Å
Salt Bridge/Ionic
Å
Contacts/Interactions
Å
Halogen Bonds
Å
π-Cation
Å
π-Stacking
Å
2. Select the first set:
3. Select the second set:
4.
Sort Interactions on:
to show interactions between two lines of residue nodes
to show interactions as map
to show interactions with strength parameters in 0-200:
Helix or Sheet:
Coil or Nucleotide:
Disulfide Bonds:
Hydrogen Bonds:
Salt Bridge/Ionic:
Contacts:
Halogen Bonds:
π-Cation:
π-Stacking:
(Note: you can also adjust thresholds at #1 to add/remove interactions.)
5. and select new sets
1. Select sets below or use your current selection:
2.
1. Select sets in two chains below or use your current selection:
2.
1. Select sets in two structures below or use your current selection:
2. Overall maximum RMSD: Å
3.
1. Select sets below:
2.
1. Select sets below:
2.
1. Select sets below:
2.
1. Select sets below:
2.
Hold Ctrl key to select multiple nodes/lines.
Green: H-Bonds; Cyan: Salt Bridge/Ionic; Grey: contacts
Note: The following parameters will be saved in cache. You just need to set them once.
1. Shininess: (for the shininess of the 3D objects, default 40)
2. Three directional lights: Key Light: (for the light strength of the key light, default 0.6) Fill Light: (for the light strength of the fill light, default 0.4) Back Light: (for the light strength of the back light, default 0.2)
The full protein sequences with gaps are listed one by one. The sequence of the structure is listed at the top. If there are non-gap residues(e.g., from RefSeq) outside of the sequence of the structure, please remove them. Each sequence has a title line starting with ">".
FASTA alignment sequences:
Position of the first residue in Sequences & Annotations window:
Color Sequence by:
BED file:
Track Title:
Track Text (e.g., "2 G, 5-6 RR" defines a character "G" at the position 2 and two continuous characters "RR" at positions from 5 to 6. The starting position is 1):
Track Title:
Name:
Please copy one of the URLs below. They show the same result. (To add a title to share link, click "Windows > Your Note" and click "File > Share Link" again.)
Original URL with commands:
Lifelong Short URL:(To replace this URL, send a pull request to update share.html at iCn3D GitHub)
Lifelong Short URL + Window Title:(To update the window title, click "Analysis > Your Note/Window Title".)
Select on 1D sequences: drag to select, drag again to deselect, multiple selection is allowed without Ctrl key, click "Save Selection" to save the current selection.
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.
Select on 3D structures: hold "Alt" and use mouse to pick, click the second time to deselect, 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" to save the current selection.
Save the current selection(either on 3D structure, 2D interactions, or 1D sequence): open the menu "Select -> Save Selection", specify the name and description for the selection, and click "Save".
Residue labeling: standard residue with coordinates: UPPER case letter; nonstandard residue with coordinates: the first UPPER case letter plus a period except that water residue uses the letter 'O'; residue missing coordinates: lower case letter.
Zoom: mouse wheel; Move: left button; Select Multiple Nodes: Ctrl Key and drag an Area
Click "View > H-Bonds & Interactions" to adjust parameters and relaunch the graph
Green: H-Bonds; Cyan: Salt Bridge/Ionic; Grey: contacts; Orange: disulfide bonds
Solvent Accessible Surface Area(SASA) calculated using the EDTSurf algorithm: (0-20% out is considered "in". 50-100% out is considered "out".)
Toal: Å2
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.
Middle Percentage(White): %
Select residue based on the percentage of solvent accessilbe surface area. The values are in the range of 0-100.
Min Percentage: % Max Percentage: %
Select residue based on B-factor. The values are in the range of 0-100.