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

Angel Herráez angel.herraez at uah.es
Tue Feb 16 15:30:38 EST 2010

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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