You may want to consider using the KiNG java applet instead of Jmol. KiNG is an implementation of MAGE, a program by David Richardson. MAGE is capable of handling many kinds of 3D data representations besides atoms, bonds, molecules. There are some Kinemages that demonstrate such uses.
http://kinemage.biochem.duke.edu/
Your proposal may well interest David ([EMAIL PROTECTED]).
Whether Jmol or KiNG best suits your project may depend on the kinds of visualizations you need. Each has its special strengths.
Good luck, -Eric
At 5/8/08, Erkki Laitila wrote:
Hi, everybody!
I have followed this topic, JMOL, because the tool seems to be nice.
However, I am not a chemist or a biologist, but an experienced computer engineer, who recently got a PhD with a topic of software reverse engineering.
I am interested in using JMOL because the atomistic model as a metaphor of my research with its software atoms, has several identical features with concrete atoms.
If anybody is interested, please look at my book here: http://dissertations.jyu.fi/studcomp/9789513932527.pdf. The cover illustrates my principal metaphor.
My elementary question to the JMOL-society is: Could JMOL be used in visualizating typical abstract concepts, e.g. typical method calls, where methods are abstract "atoms", which only have a small kernel and some links to other atoms? In the metaphor I thought that the links are like electrons of an atom.
In computer simulations, which I specify for Java, the calling atom asks information from the callees and creates new links between them. By using this dynamic information (contents of links), it is possible for the maintainer to trace program behaviour better than by using traditional methods.
An example: the method main calls methods A and B and method A calls methods A1 and A2, and B calls some BX. What kind of data format would you use in presenting these invocations in JMOL?
In my thesis I used the tool Graphviz (ATT) for making graphs. It is two dimensional, but it can automatically create positions for the nodes (a nice feature).
Motivation: If we could find a good way to present source code items in JMOL, it could be a multidisciplinary opening to connect biological information and computer science information further. There is some research for that.
PS. My final contribution in the disseration is to connect GrammarWare (presentations), ModelWare (modeling), SimulationWare (simulation for Java and others) and KnowledgeWare (capturing knowledge). This methodology is general and open to be extended into other disciplines, too. These four technology spaces work excellently in program comprehension. Perhaps they work in biology and chemistry comprehension, too?
For research information, please look at: http://www.jyu.fi/ajankohtaista/arkisto/2008/04/tiedote-2008-04-15-10-04-09-740451/
I will become happy for any suggestions how to demonstrate my small example in JMOL. Thanks!
Best regards
Erkki Laitila
SwMaster Ltd, Jyväskylä University, Finland
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Eric Martz, Professor Emeritus, Dept Microbiology
U Mass, Amherst -- http://www.umass.edu/molvis/martz
Top Five 3D MolVis Technologies http://Top5.MolviZ.Org
3D Wiki with Scene-Authoring Tools http://Proteopedia.Org
Biochem 3D Education Resources http://MolviZ.org
See 3D Molecules, Install Nothing! - http://firstglance.jmol.org
Protein Explorer - 3D Visualization: http://proteinexplorer.org
Workshops: http://workshops.proteinexplorer.org
World Index of Molecular Visualization Resources: http://molvisindex.org
ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il
Atlas of Macromolecules: http://atlas.proteinexplorer.org
PDB Lite Macromolecule Finder: http://pdblite.org
Molecular Visualization EMail List (molvis-list):
http://bioinformatics.org/mailman/listinfo/molvis-list
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