Practical Session 10

Files for practical on 3/7/2013. These files will be available for the duration of the course.
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[   ]adk_dims.dcd2013-03-07 11:53 3.7M 
[   ]adk.psf2013-03-07 11:53 910K 
[   ]Practical10Proteindynamicsandvisualization.pdf2013-03-07 11:54 688K 
[   ]1ake.pdb2013-03-07 11:53 350K 
[   ]adk_closed.pdb2013-03-07 11:53 130K 
[   ]adk_open.pdb2013-03-07 11:53 129K 
[IMG]dims_vdw.jpg2013-03-07 11:31 36K 
[DIR]ffmpeg/2013-03-07 11:31 -  
[DIR]ProteinDynamicsAndVisualization/2013-03-07 11:53 -  


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

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.