An introductory look at the molecular visualization software to 3D animation software workflow, with step-by-step tutorials to acquaint the user to three of the popular molecular viewing softwares Chimera, Pymol and VMD. Pre-production tasks done in molecular viewing software to prepare PDB files for import into Maya (via the Molecular Maya plugin) will be discussed, including splitting macromolecules into multiple pieces and rebuilding large macromolecular complexes from separate PDB files.

LEARNING OBJECTIVES

  • Discussing pros and cons of the molecular viewing software Chimera, Pymol and VMD
  • Reviewing the Chimera, Pymol and VMD interfaces
  • Performing pre-production tasks on PDB files to prepare structural data for import into Maya

TABLE of CONTENTS

01 Introduction
0:01:06
02 Pros and Cons of Molecular Visualization Pre-Production Tools
0:00:35
03 Pros and Cons of Chimera
0:02:11
04 Pros and Cons of Pymol
0:01:44
05 Pros and Cons of VMD
0:01:31
06 What 3D Graphics Software Packages Do Better
0:00:52
07 Understanding the Structure of a PDB File
0:01:32
08 Chimera Basics
0:05:48
09 Chimera - Separating Single Models into Multiple Pieces
0:04:49
10 Chimera - Building Complete Models from Multiple PDB Files
0:05:19
11 Assembling Large Macromolecules using the Multidomain Assembler Tool
0:08:57
12 Visualizing Surface Charge of a Macromolecule
0:03:21
13 Visualizing Surface Hydrophobicity of a Macromolecule
0:02:35
14 Animating Conformational Change
0:04:52
15 Pymol Basics
0:05:18
16 Pymol - Separating Single Models into Multiple Pieces
0:05:25
17 Pymol - Building Complete Models from Multiple PDB Files
0:04:06
18 Performing Mutagenesis on Macromolecules
0:02:44
19 VMD Basics
0:05:31
20 VMD - Separating Single Models into Multiple Pieces
0:04:45
21 VMD - Building Complete Models from Multiple PDB Files
0:05:01
22 Increasing the Resolution of Low Resolution PDB Files
0:02:00
23 Conclusion
0:00:59

RUN-TIME 1:22:05