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This looks very exciting. Where can we find more information about the great work that Monica is doing? Also, is there a problem with the videos? I could hear the audio fine, but the slides only changed every few minutes and did not seem to match with the audio. I tried all formats.
Dan, I think you are right about the mismatch of audio. We’ll check.
Hello Monica!
Nice presentation! Congratulations for the work so far!
As a graduate biotechnologist I completely understand the concept behind your project. It will be useful for both general public and scientists. It’s something like scientific art
About the files…
I tested the blend file. It works well except on exiting Blender (CTRL+Q) it crashes!
My favorite animation – ATP! Unfortunatelly the renderer is not Blender.
It will be nice to create a forum about the project and attract more people in solving the problems.
Regards!
Hi, glad to see you liked it. If you want to see the movie that I did not manage to show during the talk, we just uploaded on our website, together with other material (the Blender files and scripts…)
Form the site http://www.scivis.ifc.cnr.it go to Sample Works and then to Calmodulin.
Please be aware that all other material on the site is from previous work, done in Maya!!
btw, other videos (mov) also have video out of sync, too.
about monica speech, and the visualization needs: you could represent positive and negative fields with colors (which you don’t like as you said in the speech), or with object shape (fur, spikes, bumbs). or with other (surrounding your) small objects, but they could only be differenciated with shape and color. that is because sight is just made of this
anyway, you should orient your choice on “directional” properties, like gradients, for example. they have a “verse”, and this could fit the “positive/negative” force field around your object.
Your work is very interesting and useful.
It seems that you did not mention compositing. Node editor is a very powerfull tool to obtain good images. A PET scan can be compared to what you can do. Two images can be mixed in one full of sense.
I suppose that you already dispatch your data on different Layers.
Some particle’s settings can be influenced by vertex group or textures.
So creating UVs can help.
You spoke about fur,sparks,fog but axes,letters and signals are used by 3Dartists, too.
Hello Monica,
Thank-you for the great presentation and I am looking forward to looking at the files on your website. I agree with both your desire for a virtual 3d cellular environment and your decision to go with blender. I was also thinking the same thing for some time. I like to use VMD as well but find it very limiting outside of small scale molecular interactions. I also liked your idea about showing changing molecular polarity with the use of 3 layers of adjacent water molecules instead of colors. The relative strength of the magnetic field could be symbolized by how many layers of the water molecules dipole moment ‘line up’ in a specific direction. This aqueous medium could also be extended to represent the relative acid/base nature of the cellular environment. Three layers of water molecules should be sufficient around all organelles and other molecules within the cell, I would think. The 3 layers could just move with the objects in the cell. One thing that I really wish that could happen is that it would be possible to use java classes to represent objects, use molecular dynamics software to calculate potential optimal solutions or conformations, and let blender do the work of displaying the information in 3d. Finally, I would like to help if I could. I have some knowledge of blender (novice level), was a software engineer for many years, am currently completing a Masters degree in biology, and have over 20 years total college education including many other areas of specialization. If I can be of some help, let me know.
–
West
Audio has now been corrected. There was a lag with video. Thanks to Dan for pointing this out.
Hi, thanks to everyone for your comments, and (especially) to Kaveh for putting our talk up for people to see and comment, fixing the audio/video sinc.
Marco, my resistance to use color for electric potential is because i was actually thinking of using colors in different ways (if you remeber the talk, I mentioned in the end about the very many features that we are supposed to show), and also because the presence of a force can be better seen as an action, a motion of something, a dynamic visual clue rather than a property of a surface. However we are now testing many possibilities, and i suspect that color will be one of the tests.
We never thought about gradients, and the idea can be good: gradient of what (not color, eh)?
Also there is another aspect: between positive and negative (attractive and repulsive) forces, there is the zero. The effect of neutral patches of atoms on protein surfaces is to make that patch hydrophobic. This means that water moleules do not ‘like’ to stay there, and are more ‘agitated’ trying to escape, resulting in a ‘force’ that favours interaction with other protein surfaces, particularly other hydrophobic surface, excluding the water in between.
This should became evident as the result of an EP close to 0.
Ronan, i think you have many ideas, but to develop them is not a one day job!!
At the moment we have only atomic motion (and it’s been a ot of work), so we are using only 2 layers: one for the empties and one for the spheres. The next step will probably be to make metaballs from the spheres and obtain a single surface (we could take it from VMD, but it should be faster to do it in Blender).
Syziph,
thanks for the suggestion : we are setting up a forum, that might be active within this week. I will post here when it does.
For the problem on exiting, it works well for us. We use it in both 2.46 and 2.48 version.
Thank you also for the compliments! ATP is an example of B/W animation that delivers information about a very energetic molecule. I’m glad you like it.
Finally, Westly!
it would be great if a community will cooperate in developing this project. We find very important the daily exchange of ideas and information on the progressive development of work. In our group there are some biologist, bio informatics, chemist, mathematician, informatics, physicist and graphic people. The strong interdisciplinatiry of this work makes it really exciting, and also sometimes difficult just because of the different languages that we speak. In our experience this continuous direct contact has been the key that allowed tansition form a ‘collection of problems’ to a forge of solutions.
Thanks to all for your contributions, also from the other people of the group
–
Monica
well, Monica, i have a degree in phisical chemistry, rotovibrational spectroscopy (in turin)
)
so i know how tough is to think about atoms, molecules, forces, and the all…
our department need expensive silicon graphics workstations in those years…
you probably should investigate the possibilities of particle systems:
you could emit (repulsion), absorb (attraction) particles, or none if neutral.
you can create vertex groups and associate them to different particle systems.
note that particle system can also be a “reactor” to external forces, see:
http://www.blendernation.com/2008/09/26/tutorial-destroying-a-mesh-with-external-particles/
this could give you hints, i think…