[Proteopedia] Structural alignment? and other oddities whenusing multiple models in Proteopedia

Eran Hodis eran.hodis at weizmann.ac.il
Tue Feb 16 15:48:40 EST 2010

In the Authoring Tools, after a file is loaded, a command is automatically issued to Jmol to display only the first model. This is intended to make it easier to view the molecule (potentially a morph) when changing how it is displayed. It would be confusing to see all models in a morph when playing around with representations, coloring, etc.

Buttons to allow the user to change which model is viewed, view all models, or apply changes to a specific model, are absent from the Scene Authoring Tools for simplicities sake. Most users don't need to interact with multiple models. Maybe this could be implemented in some sort of advanced interface.


-----Original Message-----
>From Angel Herráez <angel.herraez at uah.es>
Sent Tue 2/16/2010 10:30 PM
To Forum for the Proteopedia User Community <proteopedialist-for-users at bioinformatics.org>
Subject Re: [Proteopedia] Structural alignment? and other oddities whenusing multiple models in Proteopedia

Wayne Decatur wrote:

> However, NOTE that if you view the scene in Proteopedia's Scene
> Authoring tool it will not show all the models even though it does on
> the actual page.

I don't now the cause of this difference (could be in the code used by the PSAT), but this 
trick could do it:
Since you are hand-editing the pdb file anyway, you can insert a Jmol command into it, so 
that anytime it is loaded all models will be displayed:

REMARK jmolscript:model all;

in any line in the file (preferably after the TITLE lines)

(This is documented at

The animations shouldn't be disturbed by this, since they will use "anim on" or "anim first" 
cancelling anyway the effect of that initial script.

I'm curious as for why some models work and others not. If you have samples, I'll be glad to 
look at them.
Again, the key may be in the exact code used by the animation tool.

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