Practical Session 10

Files for practical on 3/7/2013. These files will be available for the duration of the course.

Name	Last modified	Size

Parent Directory		-
dims_vdw.jpg	2013-03-07 11:31	36K
ffmpeg/	2013-03-07 11:31	-
ProteinDynamicsAndVisualization/	2013-03-07 11:53	-
1ake.pdb	2013-03-07 11:53	350K
adk.psf	2013-03-07 11:53	910K
adk_closed.pdb	2013-03-07 11:53	130K
adk_dims.dcd	2013-03-07 11:53	3.7M
adk_open.pdb	2013-03-07 11:53	129K
Practical10Proteindynamicsandvisualization.pdf	2013-03-07 11:54	688K

VMD

VMD is a versatile molecular visualization program. It is very good at displaying MD trajectories and is geared towards biopolymers and liquids but it can be used for a wide range of systems.

On the Macs, you will find it in /Applications.

Resources and Tutorials

VMD User's Guide
VMD Tutorial
J. Hsin, A. Arkhipov, Y. Yin, J. E. Stone, and K. Schulten. Using VMD: An Introductory Tutorial, volume 24, chapter 5.7, in Current Protocols In Bioinformatics, pages 5.7.1?5.7.48. John Wiley & Sons, Inc., 2008. doi:10.1002/0471250953.bi0507s24

Rendering with Tachyon

Example (AdK) below was rendered with Tachyon (internal) with VDW representation, colors silver, yellow, and blue, no depth cueing, material AOChalky, and using Ambient Occlusion (AO) and Shadows (see Display → Displaysettin)

Movie making

Install the ffmpeg encoder locally and use VMD's Extensions→Visualization→Movie Maker (setting Format to "MPEG-1 (ffmpeg)").

Note that you probably need to set your PATH in your ~/.profile file and completely log out and log in so that VMD will find your own ~/bin/ffmpeg binary)

You can view mpeg-1 movies simply with

open movie.mpg

MPEG-2 is better quality but Apple's QuickTime player seems to have a hard time decoding it... Linux programs tend to do better here.