how to make show color in cartoon?

[B Albert]

Hello:

I found a very nice figure which was made by bio3d:

I am just wondering how can we show the cartoon residues in various color which are consistent from network analysis? (as shown in this figure) I only see the 2d plot from:

http://thegrantlab.org/bio3d/tutorials/protein-structure-networks

but there is nothing about how we can color a cartoon.... Thank you very much.

[Xinqiu Yao]

Hi,

VMD has specific color codes for different chain IDs. The trick here is to assign a chain ID of each residue according to the community number the residue belonging to. Then, in VMD, choose the coloring method 'Chain'. I think 'vmd.cna()' (or in old bio3d versions, 'view.cna()') can do it automatically. It has been introduced in the part I of the tutorial http://thegrantlab.org/bio3d/tutorials/protein-structure-networks.

Do others have more comments?

[B Albert]

thank you for the reply.

I import network.pdb and network.vmd file into VMD. It seems work now. However, the 3D sphere from network calculation is always there and somehow hide the visualization of my cartoon. I am just wondering is it possible to hide the colorful 3D sphere from network calculation so that I can see my protein more clearly?

Thanks a lot

[Xinqiu Yao]

Hi,

Try this:

VMD menu -> Extensions -> Tk Console

In the opened terminal, type 'draw delete all'.

[Xinqiu Yao]

Have solved the user's question.