Re: [Jmol-developers] JSmol as network viewer

[Rolf H. <rh...@fl...>]

On 10/07/2014 04:50 PM, Angel Herráez wrote:
> Hi Rolf
>
> This is interesting but not what I can really discuss about, but I'd
> contribute one or two hints:
>
> One really nice thing (I've seen it in other tree viewers) would be
> the ability for the user to pull a node and have the whole thing
> rearrange dynamically. That's a force field and Jmol already does
> this with dragMinimze.
> However, probably not easy to achieve seeing the complexity of your
> trees (i.e. many "bonds" tied to an "atom").
>
Yes, Angel. It would be one of the next steps to make the layout 
directly editable by the user. It could be completely manually or 
manually-directed like you describe it. But for this you need a 
reasonable initial layout. I will keep this in mind if I ever get past 
the first step.

>> Q: Does JSmol allow that an atom is part of more than one residue or
>> would this interfere with something?
>
> Quick answer: no atom can belong to 2 residues.
>
> But I would forget about "residues". I'd just define Jmol variables
> as atom sets and assign each node to as many of them as you wish
> (using a script).
> It is as easy to select by user variables / atomsets as by residue.
> Another possibility is to assign custom atom properties, instead of
> atom sets.
>
That is what I do within the 'Jena3D Viewer' for the different mappings 
(SAPs/SNPs, PROSITE motifs etc.). And from there I know that commands 
can be very slowly this way. Handling for example several hundred SNPs 
by using sets already takes quite some time (see for example 
http://jenalib.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=1A00&APPLET=HTML5). 
And in the network viewer the number of sets would potentially be much 
higher. It will also require to rebuild a lot of built-in functions to 
get similar (slower) functionalities.

Regards,
Rolf
-- 

Rolf Huehne
Postdoc

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