Visualization of proteins

By rparkesh at Fri, Feb 27 2009 10:54am |

General Discussion

HI
I was wondering if anyone has used some kind of external hardware apart from mouse to better visualize proteins and protein-ligand interaction in e.g Pymol. I was trying with Nintendo wii and a sensor bar. It is great to view but the control is very fuzzy. I had also some fun with 3D connexion which is great with 3D application such as Maya, Autocad etc but i am not sure if it will work with Pymol or other programs.

Has any one used other devices? The input will be really helpful.

Cheers
Raman

Fri, 2009-02-27 13:00 — drc

Zodiac

Have a look at Zodiac

http://homepage.mac.com/swain/Sites/Macinchem/page11/page11.html

Mon, 2009-03-02 05:30 — rparkesh

Re:

That sounds interesting. But are these hepatic devices cheap. I was checking in the internet and they cost around $20,000 dollar.
That will limit their application as visualization tools.

Regards
Raman

Mon, 2009-03-02 06:11 — zontan

Haptic Devices

Actually you can get an haptic device for as low as 200 GBP (around 300 $).
http://home.novint.com/

Or if you need a more professional one the sensable Phantom should be around 1500 $
http://www.sensable.com/

you can find some info and videos on the use of those devices on my website
www.zeden.org

also, you might be interested in reading the following:
http://www.ncbi.nlm.nih.gov/pubmed/19048316?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum

Nicola Zonta
nicola.zonta@zeden.org

Mon, 2009-03-02 17:28 — rcomeau

SpaceNavigaotr

Hi,

The issue will likely be what 3D input devices are supported by the software. In CAD, there is a SpaceNavigator which I have seen a CAD designer friend use an really love.

Roch Comeau
Rogue Reseach Inc.

Tue, 2009-03-03 06:14 — rparkesh

Re:

I think these devices are really great. Now it gives power to the medical chemist to use their intuition and chemistry knowledge to design better drugs or analogs.

This will be really useful when you are docking ligands into the binding site. You can explore the interaction and modify the structure accordingly.

I have recently seen in pymol site (www.pymol.org) now you have really affordable 3D monitor.
I think now if you can dive deep into proteins using e.g spacenavigator you can have a better fell of the binding pocket and that will be useful for docking and drug design.

Thanks
Raman

Tue, 2009-03-03 06:55 — drc

The Zalman ZM-M220W LCD Display for Stereo 3D Visualizatio

Has anyone tried this out?
http://www.zalman.co.kr/eng/product/Product_read.asp?Idx=219

at £417 for a 22 inch screen it is not that inexpensive.

Mon, 2009-03-30 05:42 — nicola_zonta

Zalman

I'm currently using the zalman monitors with a sensable phantom device and Zodiac to do fragment-based drug design. here are some movies..

http://www.youtube.com/watch?v=cbjrUY6Ej50
http://www.youtube.com/watch?v=0Nl_NJfXyJ4

the monitors are really good. 3D helps a lot even though you lose in resolution. Anyway I think they are really good value for money.

If anybody is interested in testing the application of haptic devices to drug design, I'm looking for collaborators.. please drop me an email

nicola_zonta@zeden.org

Nicola Zonta

Tue, 2009-12-08 18:32 — LeninWTigger

3D connexion Space Navigator.

So far I know that the Space Navigator (http://www.3dconnexion.com/products/spacenavigator.html) works with MacPymol (and the X11 Hybrid) as well as UCSF Chimera (http://www.cgl.ucsf.edu/chimera/ , I only use the X11 version so I am not sure about its functionality on the Aqua version).

Does anybody knows of any other scientific visualization software that takes advantage of the Space Navigator?

MacResearch