[Chimera-users] Sampling the density of a map in the vicinity of each atom in a model

[Tom Goddard]

Hi Mario,

  I just remembered I wrote a little Python to average map values in a sphere around atoms, called mapsum.py on the Chimera Python scripts web page:

	http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts <http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts>

  Tom


> On Mar 22, 2015, at 10:41 AM, Mario J. Borgnia <mborgnia at helix.nih.gov> wrote:
> 
> Hi,
> I have a density map in mrc format and a model in pdb format. I would
> like to calculate the average density within a 3D window centered at the
> coordinates of each atom in the model and include the result as an
> attribute for the atom. Despite some effort searching for the answer, I
> cannot find out how to do this easily. I could try and go deep into
> Python programming but, before I reinvent the wheel, I'd like to know
> whether there already is a simpler way to do this in Chimera.
> 
> Thanks!
> 
> Mario
> 
> 
> -- 
> +---------------------------------+
> | Mario J. Borgnia, Ph. D.        |
> |                                 |
> | Lab of Cell Biology             |
> | NIH NCI/CCR                     |
> | 50 South Drive Rm 4306 MSC 8008 |
> | Bethesda MD 20892-8008          |
> |                                 |
> | Tel: (301) 594 0563             |
> | mborgnia at nih.gov                |
> +---------------------------------+
> 
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