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Author Topic: Jmol as an alternative for visualization?  (Read 3876 times)

Offline xiangjun

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Jmol as an alternative for visualization?
« on: December 09, 2008, 02:35:29 pm »
Hi Guohui,

I noticed that you are using WebMol for visualization, which is fine. However, you might consider to add Jmol as an alternative, at least. Jmol seems to be quite popular right now with an active community. I have recently asked a question regarding Jmol support on alchemy file format there, and received near ten responses.

Also, for the fiber models, I thought we could have a page with all 55 models each with images in (three) different views, citations to the original references etc. This will give users a direct impression on the comprehensiveness of possibilities available with w3DNA/3DNA. We certainly have no matches, as far as I am aware of. A handy (robust and efficient) fiber-model generation and visualization service will by itself be a useful tool to community at large (e.g., for educational purpose), as I mentioned to you before.

Thanks for answer questions in the open 3DNA forum. You will realize that it is good thing to do: just keep doing it!

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline ghzheng

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Re: Jmol as an alternative for visualization?
« Reply #1 on: December 09, 2008, 02:50:34 pm »
Hi Xiangjun,

I would like to offer various visualization tools, including Jmol, King etc., which I am working on.

Regarding to the fiber model construction, Wilma suggested generate a fiber with combination of different fiber models, such as 5 repeats A form + 5 repeats B form. We understand that the difficulty is the connection of two fiber models (backbones). What do you think of having this option on our web server?

Thanks.

Guohui

Offline xiangjun

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Re: Jmol as an alternative for visualization?
« Reply #2 on: December 09, 2008, 04:57:14 pm »
Quote from: "guohui"
Regarding to the fiber model construction, Wilma suggested generate a fiber with combination of different fiber models, such as 5 repeats A form + 5 repeats B form. We understand that the difficulty is the connection of two fiber models (backbones). What do you think of having this option on our web server?

I understand Wilma's point, but I honestly do not think it is a good idea here. There are could possibly be many different combinations of the various fiber models, which could be very creative, but  arbitrary. This is exactly what I want to avoid in this work, but it could possibly be left to another paper.

Basically, this is not a scientific paper, but a web-interface to commonly used functionality in 3DNA, and we've already had many stuffs to offer. Additionally, as a general design principle, the web-interface should be simple, targeting the non-expert users. Power-users will play directly with the command-line version.

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.