[ghemical-devel] Selection mode

[Tommi Hassinen]

On Mon, 5 Jun 2006, Claudio Forcato wrote:

> We want to introduce a new selection mode, with which you can select
> secondary structure, as alpha-helix or beta-sheets.
> Do you think should be quite easy or not?
>
> Could you point us to the right piece of code that manages the
> contextual menu and in particular the selection mode?

Hello!

Selecting based on secondary structures would mean that the secondary 
structural elements are first identified. Such code already exists, but I 
don't think it fits into this purpose well since it is rather slow (it 
detects secondary structure elements by looking for hydrogen bonds ; so 
finding beta-sheets can take several minutes). So this is bad in an 
interactive selection operation.

You can find the code if you look how the protein ribbon models are drawn 
(the ribbon width is set wider for helices and sheets).

Instead of selections based on secondary structures, I have planned a new 
2D-view for protein structures. Such a view would show the protein chains 
as horizontal lines or "pearl strings", using colours to display the 
secondary structures. Several protein chains would then be shown as 
stacked lines. Such a display would make also selection operations 
easier as they are now.

I'm happy that you have found ghemical useful also in work with proteins! 
I certainly would like to help you, since that is an important area for me 
as well.

> Is there a manual to hack on ghemical?

Sorry, no. You just have to browse the source code...

Regards,

 	Tommi