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  • All atoms  Selection  
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Defined Sets:
Set Operations:




Select:
Name:
   
Specification Tips:

Specification: In the selection "$1HHO,4N7N.A,B,C:5-10,KRDE,chemicals@CA,C":
  • "$1HHO,4N7N" uses "$" to indicate structure selection.
  • ".A,B,C" uses "." to indicate chain selection.
  • ":5-10,KRDE,chemicals" uses the colon ":" to indicate residue selection. Residue selection could be residue number (5-10), one-letter IUPAC abbreviations (KRDE), or predefined names: "proteins", "nucleotides", "chemicals", "ions", and "water". IUPAC abbreviations can be written either as a contiguous string (e.g., ":KRDE"), in order to find all instances of that sequence in the structure, or they can be separated by commas (e.g., ":K,R,D,E") to select all residues of a given type in the structure (in the latter case, select all Lysine, Arginine, Aspartic Acid, and Glutamic Acid 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,KRDE,chemicals@CA,C
  • Select and save: select $1HHO,4N7N.A,B,C:5-10,KRDE,chemicals@CA,C | name my_name
Select:
Name:
   
Specification Tips:

Specification: In the selection "$1HHO,4N7N.A,B,C:5-10,KRDE,chemicals@CA,C":
  • "$1HHO,4N7N" uses "$" to indicate structure selection.
  • ".A,B,C" uses "." to indicate chain selection.
  • ":5-10,KRDE,chemicals" uses the colon ":" to indicate residue selection. Residue selection could be residue number (5-10), one-letter IUPAC abbreviations (KRDE), or predefined names: "proteins", "nucleotides", "chemicals", "ions", and "water". IUPAC abbreviations can be written either as a contiguous string (e.g., ":KRDE"), in order to find all instances of that sequence in the structure, or they can be separated by commas (e.g., ":K,R,D,E") to select all residues of a given type in the structure (in the latter case, select all Lysine, Arginine, Aspartic Acid, and Glutamic Acid 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,KRDE,chemicals@CA,C
  • Select and save: select $1HHO,4N7N.A,B,C:5-10,KRDE,chemicals@CA,C | name my_name
MMTF ID:
PDB ID:
Orientations of Proteins in Membranes(OPM) PDB ID:
PDB File:
Enter the PDB IDs or MMDB IDs of two structures that have been found to be similar by VAST+ :

ID1:       ID2:

   
Enter the PDB chain IDs in the form of pdbid_chain (e.g., 1HHO_A, case sensitive):

ID1:       ID2:

Mol2 File:
SDF File:
XYZ File:
File type:
URL in the same host:
mmCIF File:
mmCIF ID:
MMDB or PDB ID:
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):
Protein gi:
PubChem CID:
iCn3D PNG image:
State file:
Selection file:
Note: Always load a PDB file before loading DSN6 files.


2fofc contour at: σ



fofc contour at: σ




Click in the input box to use the color picker:

Custom Color:
1. Choose interaction types and their thresholds:
Hydrogen Bonds   Salt Bridges   Contacts/Interactions  
Threshold: Å
Threshold: Å
Threshold: Å
2. Select the first set:

3. Select the second set:

4. H-bonds/Contacts in 3D

H-bond/Contact pairs in a window

H-bond/Contact pairs in a file

and select new sets
Contour at: σ
Contour at: σ
Contour at: % of maximum EM values
1. Select the first set:

2. Sphere with a radius: Å

3. Select the second set to apply the sphere:

4. the sphere around the first set of atoms

interacting/contacting residue pairs in a file
Note: The membranes are parallel to the X-Y plane. The center of the membranes is at Z = 0.

1. Extracellular membrane Z-axis position: Å

2. intracellular membrane Z-axis position: Å

3. the adjusted membranes

Note: The membranes are parallel to the X-Y plane. The center of the membranes is at Z = 0.

1. Z-axis position of the first X-Y plane: Å

2. Z-axis position of the second X-Y plane: Å

3. the region between the planes to Defined Sets

1. Text:
2. Size:
3. Color:
4. Background:
5. Pick TWO atoms while holding "Alt" key
6.
1. Text:
2. Size:
3. Color:
4. Background:
5.
1. Pick TWO atoms while holding "Alt" key
2. Color:
3.
1. Pick TWO atoms while holding "Alt" key
2. Color:
3.
1. Pick TWO atoms while holding "Alt" key
2.
Line Radius:    (for stabilizers, hydrogen bonds, distance lines, default 0.1)
Coil Radius:    (for coils, default 0.3)
Stick Radius:    (for sticks, default 0.4)
Trace Radius:    (for C alpha trace, O3' trace, default 0.2)
Ribbon Thickness:    (for helix and sheet ribbons, nucleotide ribbons, default 0.2)
Protein Ribbon Width:    (for helix and sheet ribbons, default 1.3)
Nucleotide Ribbon Width:    (for nucleotide ribbons, default 0.8)
Ball Scale:    (for styles 'Ball and Stick' and 'Dot', default 0.3)
Line Radius:    (for stabilizers, hydrogen bonds, distance lines, default 0.1)
Coil Radius:    (for coils, default 0.3)
Stick Radius:    (for sticks, default 0.4)
Trace Radius:    (for C alpha trace, O3' trace, default 0.2)
Ribbon Thickness:    (for helix and sheet ribbons, nucleotide ribbons, default 0.2)
Protein Ribbon Width:    (for helix and sheet ribbons, default 1.3)
Nucleotide Ribbon Width:    (for nucleotide ribbons, default 0.8)
Ball Scale:    (for styles 'Ball and Stick' and 'Dot', default 0.3)
  • NCBI gi/Accession
  • FASTA
  • BED File
  • Custom
  • Current Selection
NCBI gi/Accession:

FASTA Title:

FASTA sequence:


BED file:

Track Title:

Track Text (e.g., "152 G, 155-156 RR" defines a character "G" at the position 152 and two continuous characters "RR" at positions from 155 to 156. The starting position is 1):


Track Title:

Name:


Please copy one of the URLs below. They work the same way.

Original URL with commands:


Short URL:


  • Summary
  • Details
Annotations: 
All   Conserved Domains   ClinVar   Functional Sites   Disulfide Bonds  
Custom   3D Domains   SNPs   Interactions   Transmembrane  


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: 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.