Advanced VMD Visualization

Find sequences of protein structures by Multiseq plugin

Multiseq plugins in the VMD software helps you to find the sequence and structure of biomolecules and proteins.
To access Multiseq: Extensions ----> Analysis ----> Multiseq
This plugin helps you to choose specific sequences or residues in your structure and visualize them specifically.

VMD Contact Map plugin helps you to find residue-residue contact in two different or same set of biomolecules and visualize it as a matrix.
To access VMD Contact Map: Extensions ----> Analysis ----> VMD Contact Map
Contact map is important for analysis of residues in proteins to see which sequences are in contact with each other. Contact map of proteins could be considered as their signature for identifying different biomolecular structures.

Another VMD plugin is Hydrogen Bonds, that help you to identify hydrogen bonds between a set of atoms based on a pre-defined criteria in each frame of molecular dynamics results.
To access Hydrogen Bonds plugin: Extensions ----> Analysis ----> Hydrogen Bonds
In the Input options section, choose the molecule that you want to use for Hydrogen bonds calculation, and specify Donor-Acceptor distance as well as Angle cutoff as criteria for finding the bonds.
Note that you need to load ubiquitin.psf and pulling.dcd to be able to run Hydrogen Bonds plugin.

VMD can calculate Radial Pair Distribution Function for molecular dynamics results for two selections of a molecular structure.
Note that you need to load ubiquitin.psf and pulling.dcd to be able to run this plugin.
To access Radial Pair Distribution Function: Extensions ----> Analysis ----> Radial Pair Distribution Functions
Select the selections and then specify the frames that you want to use for radial distribution function calculations.

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