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

[Thomas Goddard]

Hi Miguel,

   For creating the volume occupancy map the molmap command creates a 
volume by placing a Gaussian centered at each atom.

http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html

The Gaussian width is set by the molmap resolution parameter and is the 
same for all atoms.  It does not use vdw radii.  If you want to use vdw 
radii and if you want to sum over many torsion angles you might use a 
modified version of the molmap Python code.  See the 
molecule_grid_data() routine in file

	chimera/share/MoleculeMap/molmap.py

in your Chimera distribution.

	Tom




> 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
>> <http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/Scripts>). 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
>>> Web: http://www.pangea.org/mol/spip.php?rubrique2
>>>
>>>
>>> <C3vol.png><torspace.py>
>>>
>>>
>>
>>
>> --
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>
> -- 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
> Web: http://www.pangea.org/mol/spip.php?rubrique2
>
>
>
>
>