Topics covered in this tutorial includevisualizing molecules in three dimensions with different drawing and coloringmethods, rendering publication-quality figures, animate and analyze the trajec-tory of a molecular dynamics simulation, scripting in the text-based Tcl/Tkinterface, and analyzing both sequence and structure data for proteins.īefore staring the tutorial you need to download the current version of VMD.This tutorial requires VMD version 1.9 or later. It is impossibleto cover all of VMDs capabilities, but here we will present several step-by-step examples of VMDs basic features. This article will serve as an introductory VMD tutorial.
#Vmd tutorial movie
Molecular analysis commands Rendering high-resolution, publication-quality molecule images Movie making capability Building and preparing systems for molecular dynamics simulations Interactive molecular dynamics simulations Extensions to the Tcl/Python scripting languages Extensible source code written in C and C++ General 3-D molecular visualization with extensive drawing and coloringmethodsĮxtensive atom selection syntax for choosing subsets of atoms for display Visualization of dynamic molecular data Visualization of volumetric data Supports all major molecular data file formats No limits on the number of molecules or trajectory frames, except availablememory Amongmolecular graphics programs, VMD is unique in its ability to efficiently operateon multi-gigabyte molecular dynamics trajectories, its interoperability with alarge number of molecular dynamics simulation packages, and its integration ofstructure and sequence information. It is developed by the Theoretical and ComputationalBiophysics Group at the University of Illinois at Urbana-Champaign. VMD (Visual Molecular Dynamics) is a molecular visualization and analysisprogram designed for biological systems such as proteins, nucleic acids, lipidbilayer assemblies, etc. 586.2 Example of a built-in analysis tool: the RMSD Trajectory Tool. 535.2.2 Importing FASTA files for sequence alignment. 525.2.1 Aligning molecules and coloring molecules by degree ofĬonservation. 495.1.3 Coloring molecules by their structural identity.
46ĥ Comparing Structures and Sequences with MultiSeq 485.1 Structure Alignment with MultiSeq. 44Ĥ.2 Aligning Molecules with the measure fit Command. 434.1.3 Drawing different representations for different molecules. 40Ĥ Working with Multiple Molecules 424.1 Main Menu Molecule List Browser. 353.2.3 Obtaining and changing molecule properties with textĬommands. 34ģ.2.1 Loading molecules with text commands. 30ģ Scripting in VMD 323.1 The Basics of Tcl Scripting. 23Ģ Trajectories and Movie Making 252.1 Loading Trajectories. 171.6 The Basics of VMD Figure Rendering. 131.3.4 Creating multiple representations. 101.3.2 Exploring different coloring methods.
10ġ.3.1 Exploring different drawing styles. Join the mailing list for additional help.ġ Working with a Single Molecule 81.1 Loading a Molecule. Lee, Zan Luthey-Schulten, Patrick ODonoghue, ElijahRoberts, Anurag Sethi, Marcos Sotomayor, Emad Tajkhorshid,Leonardo Trabuco, Elizabeth Villa, Yi Wang, David Wells, DanWright, Ying YinĢA current version of this tutorial is available at Tutorial Contributors:Alek Aksimentiev, Anton Arkhipov, Robert Brunner, JordiCohen, Brijeet Dhaliwal, John Eargle, Jen Hsin, Fatemeh Khalili,Eric H. University of Illinois at Urbana-ChampaignBeckman Institute for Advanced Science and TechnologyTheoretical and Computational Biophysics GroupComputational Biophysics Workshop