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

Tom Goddard goddard at sonic.net
Mon Mar 23 09:56:51 PDT 2015


Hi Mario,

  An approach to this is to simply Gaussian smooth the map (vop gaussian command), then use the Values at Atom Positions tool.  The Gaussian smoothing replaces the value at each grid point with a weighted average of nearby grid values with a Gaussian fall-off of weights with distance from the atom.  You said “windowing” which usually means you make a hard cutoff, you use an unweighted average within a box centered at an atom, or within a sphere centered at an atom.  For most uses I think the soft cutoff of a Gaussian weighting with distance is better than hard cutoff.  If you really want the hard-cutoff and unweighted averaging it would require Python programming.

	Tom


> On Mar 22, 2015, at 10:41 AM, Mario J. Borgnia 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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