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Generate plot: Button to plot the selected centrality.Ĭolor by: Option to color the nodes in network 3d view.ĭefault: Nodes are colored based on chain id. Sort by: Option to sort the centrality display table based on residue or Network image: Save the network image in PNG format.Ĭentrality: Option to select centrality from drop down menu. Structure image: Save the structure image in PNG format. Hydrophilic:Highlight hydrophilic residues and show edges only between them.Ĭharged:Highlight charged residues and show edges only between them. Hydrophobic:Highlight hydrophobic residues and show edges only between them. JSmol view are highlighted in yellow color.Īll residues:Display all residues and endges between them.
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The neighboring nodes in the network view and the corresponding residues in Neighbors: On selecting a node in the 3D network view, the node and the corresponding residue in Node: On selecting a node in the 3D network view, the node and the corresponding residue in Highlight selection: Active only for Network 3D view. Network 3D: 3D representation of the network with node coordinates representing the actualĭistance matrix: 2D distance matrix view. A value in the range 1-15 can be selected. Sequence to be considered for network construction. Residue separation: Minimum separation of residues in the protein Range of distance to be considered for the construction of an edge between a pair of nodes (residues).įor "Interaction strength" (IS) type network, only the lower bound interaction strength (in %) is taken as input.Īn edge is constructed if the interaction strength is greater than the given threshold. Threshold: The lower and higher cutoff distance (in Å) determines the Weighted: Weights are assigned to the edges depending on different criteria for different network types:Ī) C-alpha: Inverse of distance between C-alpha atoms.ī) C-beta: Inverse of distance between C-beta atoms.Ĭ) Any atom: Number of atom pairs within threshold distance.ĭ) Centroid: Inverse of distance between centre of mass of the residues.Į) Interaction strength: Interaction strength between the residues. All edges are considered equally important. Unweighted: No weight is assigned to the edges. Interaction strength:An amino acid residue is considered as node in the network and an edge isĬonstructed if the interaction strength between two residues is more than the threshold defined by the user. Side chain is considered as node in the network and an edge is constructed if the distance between centroids is less than the The default threshold is 5 Å.Ĭentroid (centre of mass): An amino acid residue represented by the centre of mass (centroid) of the In the network and an edge is constructed if the distance between any pair of atoms of the residue pair is less than 'A' is considered different from 'a'.Ĭ-alpha: An amino acid residue represented by the C-alpha atom is considered as node in the networkĪnd an edge is constructed if the distance between the C-alpha atoms is less than the threshold defined by the user.Ĭ-beta: An amino acid residue represented by the C-beta atom is considered as node in the networkĪnd an edge is constructed if the distance between the C-beta atoms (C-alpha for GLY) is less than the threshold defined byĪtom pair contact: An amino acid residue represented by the centre of residue is considered as node In case of analysis of protein complex, Chain 1 and Chain 2 represent the two proteins in complex. Two chains: Analyze two proteins (protein complex) represented by two different chains in PDB file.Ĭhain: Chain id of PDB file which represents the desired protein. Single chain: Analyze protein represented by one chain in PDB file. One of the following options can be selected: PDB: Provide the PDB id or upload PDB file.Īnalyze (analysis type): Determines the type of analysis to be performed.