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

[Eric Pettersen]

Hi Miguel,
	For finding clashes you would use the detectClash() method in the  
DetectClash module.  It has a pretty long doc string so I think it  
will be clear how to call/use it.

> Also, just a question: is there a way to access bonds as part of a  
> tree? I would like to select the atoms implicitly from the list of  
> bonds to be rotated.

	I'm reading this as:  for a given torsion, what are the atoms that  
will be rotated?  There is a function of Molecule (m.traverseAtoms())  
that returns atoms in traversal order.  Furthermore, that function can  
ignore (i.e. cross) "break points" (active torsions) or not cross  
them.  That is the function you would use, but you would need to  
restructure your code so that you only have one torsion active at a  
time rather than all of them.  Here's a loose outline:

# activate torsion
br = bondRotMgr.rotationForBond(b)

# which atom is opposite the "anchor" side of the torsion (anchor ==  
unmoving side)
ma = b.otherAtom(br.anchorSide)

# what is the "root" for graph-traversal purposes on that side
root = ma.molecule.rootForAtom(ma, False) # the "False" means don't  
ignore active torsions

# list of atoms on that side
myatomlist = ma.molecule.traverseAtoms(root)

...do the stuff that drives the torsion...

# deactivate torsion
br.destroy()

--Eric

On May 13, 2010, at 4:13 AM, Miguel Ortiz Lombardia wrote:

> Hi Eric and Tom,
>
> Thank you! Yes, I would like to improve the script so, it would be  
> great if you can give me pointers about clashes and filling the VDW  
> space!
>
> Also, just a question: is there a way to access bonds as part of a  
> tree? I would like to select the atoms implicitly from the list of  
> bonds to be rotated.
>
> Best regards,
>
>
> Miguel
>
> Le 13 mai 2010 à 02:15, Eric Pettersen a écrit :
>
>> Hi Miguel,
>> 	The script still is pretty useful!  I've added it to the "Python  
>> Scripts" page on our wiki (Scripts – Chimera). You are right that  
>> improvements could be made, but it's a nice starting point.  If you  
>> ever decide to refine the script, I could probably provide pointers  
>> on finding clashes, whereas Tom Goddard (whom I've cc'ed) would  
>> probably have to be the one to assist in filling a grid based on  
>> the atom's VDW radius (presumably scaling a three-dimensional  
>> gaussian or some such).
>>
>> --Eric
>>
>> On May 12, 2010, at 1:46 PM, Miguel Ortiz Lombardia wrote:
>>
>>> Le 12 mai 2010 à 19:00, Eric Pettersen a écrit :
>>>
>>>> Hi Miguel,
>>>> 	I'm glad you got everything sorted out.  Good luck.  Feel free  
>>>> to shoot me any further questions you might have.
>>>>
>>>> --Eric
>>>>
>>>
>>> Hi Eric,
>>>
>>> Thanks! I managed to make it work. I'm attaching the script in  
>>> case you or someone may find it useful. There is only a point I  
>>> haven't managed to solve: as it is, the script creates a grid  
>>> point at the atom center positions, while I would be more  
>>> interested in the van der Waals volume. Nevertheless, since this  
>>> is a very naive approach (it would be more interesting, for  
>>> example, to avoid any clashes) I'm using an external set of  
>>> programs (mapman and mama from the "Uppsala Software Factory") to  
>>> extend this volume by a couple of grid points.
>>>
>>> I'm attaching as well a figure so you see how it looks like (after  
>>> expansion with mapman/mama).
>>>
>>> Thanks for your advice, I have learnt a lot from this exercise.
>>>
>>> Best regards,
>>>
>>>
>>> -- Miguel
>>>
>>> Architecture et Fonction des Macromolécules Biologiques (UMR6098)
>>> CNRS, Universités d'Aix-Marseille I & II
>>> Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
>>> Tel: +33(0) 491 82 55 93
>>> Fax: +33(0) 491 26 67 20
>>> e-mail: miguel.ortiz-lombardia at afmb.univ-mrs.fr
>>> Web: http://www.pangea.org/mol/spip.php?rubrique2
>>>
>>>
>>> <C3vol.png><torspace.py>
>>>
>>>
>>
>>
>> -- 
>> This message has been scanned for viruses and
>> dangerous content by MailScanner, and is
>> believed to be clean.
>
> -- Miguel
>
> Architecture et Fonction des Macromolécules Biologiques (UMR6098)
> CNRS, Universités d'Aix-Marseille I & II
> Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
> Tel: +33(0) 491 82 55 93
> Fax: +33(0) 491 26 67 20
> e-mail: miguel.ortiz-lombardia at afmb.univ-mrs.fr
> Web: http://www.pangea.org/mol/spip.php?rubrique2
>
>
>
>
>

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