Biomolecules: Databanks, Visualisation and Computations -Lecture Material


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Demonstration material and scripts

The VMD-based demonstrations and the molecular vibration examples shown during the lectures on Biophysical Chemistry are included in the zipped script collections 'vmdscripteng.zip' and 'viblogfiles.zip' or the resp. *.tar.gz files. The scripts are also available with german button text. If you use these resources, I would appreciate getting a notification.

VMD scripts

VMD-scripts for download. Most include button control, which allows for fast switching between presentations and are therefore particularly suitable for use in lectures and talks. Another option is to apply these scripts in an elearning environment. The hypertext buttons that contain a longer comment to each representation are particularly suitable to this end.
Take a look at some screenshots showing VMD with button controlled presentations.
Some of the scripts can also be used in high-school or for science fairs,. These contain proteins of general interest such as antibodies, photosynthetic systems, proteins of the vision process etc. An additional description on these proteins with background information is also available. (vmdteach.pdf) , also available in german (vmdlehre.pdf)

Read installation instructions file prior to using the following zipped VMD example script files !

VMDscript Installation and Content     
VMDscript_Installation and Content     

Further, there is a more thorough manual available, that also describes how to create own scripts of this kind:


The following are the packed script files. The zip- files and the tar.gz -files have identical content, please only download the one that is most convenient for you:

vmdscripteng.tar.gz, updated 14th may 08
vmdscripteng.zip, updated 14th may 08

The scripts should be usable with any OS for which VMD is available. The scripts are also available with german explanation buttons (click here).

Vibrational mode visualizations

Molecule calculation results for vibrational mode visualisation with molden and molekel as used in the lecture 'Biophysical Chemistry'. Molden was used in the lecture, because it does not only show vibrational mode animation, but also shows the IR and Raman spectra. Take a look at some screenshots.

Download viblogfiles.tar.gz

Chime Scripte

You find information concerning the usage of the Chime -Plug-in here. There are also links to additional external pages . Note that MDL-Chime officially only supports some types of browsers such as Netscape 4.7x or some versions of IE. Unfortunately with IE, many examples do not work properly. However you can also install MDL-Chime in connection with Mozilla, Firefox and Netscape, see here.

For questions, please contact:
Peter Schellenberg, phone (+351) 253-604074

Peter Schellenberg may 22nd 2008