[chimera-dev] Volume covered by a group of atoms

[Eric Pettersen]

On May 15, 2010, at 2:29 PM, Miguel Ortiz Lombardia wrote:

> I'm afraid I don't clearly understand the concept of "active  
> torsion" in the context of the script. What I do is to read the  
> first torsion and assume it is the root of all the torsions to be  
> rotated about so it can be used to select the atoms that will move  
> in the way you showed. Then I create my 'torsionlist' as before. It  
> seems to work.

You can't increment or otherwise work with a torsion after you've  
destroyed it -- that's why you got an error. I assumed you would use  
the torsion just to determine the atom list, not try to continue to  
use it after the destroy() call.  Therefore, in the context of your  
script it is correct not to call destroy, as you found out through  
experimentation.

All the torsions you've created and not yet called destroy() on are  
"active".  That means that each one is a "break point" as far as graph  
traversal is concerned.  Therefore the way you went about it --  
activating only one torsion, getting the atom list, then activating  
the other torsions -- gives you the right list of atoms.  If you had  
activated all the torsions before asking for the list of atoms you  
would have had trouble.

--Eric


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