[Chimera-users] suggestion

Thomas Goddard goddard at cgl.ucsf.edu
Thu Nov 16 19:24:43 PST 2006

Hi David,

  Thanks for your suggestion to add coloring of isosurfaces based on
gradient magnitude to Chimera.  I think I can add this to the Surface
Color tool in an hour or two since the gradient calculation code is
already in Chimera (for fitting atomic models in maps).  I'll try to
put it in soon and send you the code to test.

Description of coloring from article:

    "OpenDX (www.opendx.org) module MAKROVIS was implemented to create
     masks of different shapes and to analyze disorder in the
     reconstructions (Figure 1B). For this, isosurface rendering of a
     given voxel was colored as a function of the maximum density
     difference between the voxel and its neighbors."


> From: "David G. Morgan" <dmorgan at ucdavis.edu>
> To: goddard at cgl.ucsf.edu
> Subject: suggestion
> Date: Thu, 16 Nov 2006 19:03:50 -0800
> Tom,
> I have a suggestion for the developers "list of ideas to implement," if
> you think there would be enough interest from users and that it is
> something that chimera should do.  I realize that you get lots of
> suggestions, and that some of them are simply outside the realm of what
> the chimera developers think chimera is intended to do.  But since you
> do ask for suggestions, here's my most recent one.
> I'm attaching a recent journal article where the authors used a color
> coding scheme to display "order/disorder" regions of an EM
> reconstruction.  The images are in Fig 1 B and the rather sparse
> description of the "algorithm" is a single sentence in the "Image
> Processing 3D Reconstruction" section (p 1046).  The idea of color
> coding some estimate of the better defined regions of a density map is
> very nice (and clever), and would be extremely helpful in lots of
> situations (my plug for wanting you guys to implement something
> similar...).
> The idea behind this is that for any given region of iso-surface, the
> density gradient normal to that surface should be a reasonable measure
> of how well defined the density is.  In other words, a very steep
> gradient (e.g., a fast transition between protein and solvent) means
> very well defined density and a flat gradient means weakly defined
> density (disordered regions, partial occupancy, etc.).  The authors
> don't do such a complicated calculation, but it seems that what they
> implemented at least captures most of this sort of character.
> I think the key to this is that the gradient is calculated "locally."
> I've looked at gradients as a function of resolution with the idea of
> using it to help chose a proper iso-surface.  While it works well with
> model data, real reconstructions aren't nearly so well behaved.  I
> hadn't thought about this in a while, but I think what the authors have
> done both helps explain the behavior of my real data (the gradient is
> simply too varied) and is a quite useful visualization tool.
> So please think about implementing something like this in the volume
> handling tools of chimera.
>                     David Gene Morgan
>              Advanced Microscopy & Proteomics
>                 Molecular & Cellular Biology
>              University of California at Davis
>                     530 752 2693 (lab)
>                     530 752 3085 (FAX)
> ----
> removed PDF for 
> Huiskonen JT, de Haas F, Bubeck D, Bamford DH, Fuller SD, Butcher SJ.
> Structure of the bacteriophage phi6 nucleocapsid suggests a mechanism for sequential RNA packaging.
> Structure. 2006 Jun;14(6):1039-48. 

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