[Chimera-users] Contour maps or step-gradient of volume map?

Tom Goddard goddard at sonic.net
Mon May 13 11:02:49 PDT 2013


Hi Esther,

  Here are example commands that open a map, show two contour levels 0.8 blue, and 1.0 yellow, and clip perpendicular to the z axis with a slab of thickness 10 Angstroms.

open emdbID:1080
volume #0 level .8 color blue level 1 color yellow
mclip #0 axis z coord local origin 0,0,0 slab true thickness 10

This doesn't look good though because the blue and yellow flat surfaces at the clip plane are exactly overlapped so the graphics shows one or the other based on floating point round-off errors and it looks like a scrambled set of triangles.  So your "kludge" method is in fact better.  Here's an example of that.

open emdbID:1080
vop scale #0
volume #0 level 0.8 color blue
volume #1 level 1.0 color yellow
mclip #0,1 axis z coord local origin 0,0,0 slab true thickness 10 stagger 0.5

The "vop scale #0" copies volume 0 (scales it by default factor = 1).  The mclip command now has the extra "stagger 0.5" option to offset the clip planes of the different models by 0.5 Angstroms.

  I've attached pictures of the results of these two methods.

  When using the volume dialog you can add extra contour levels by ctrl-click on the histogram.

	Tom



On May 8, 2013, at 3:04 PM, Bullitt Esther wrote:

> Hi,
> 
> Is it possible to choose n levels of gray for a volume map?  I'd like to make a known-thickness slice using clip, and then see that slice as a defined number of colors.
> 
> I can kluge it by displaying the map 4 times at 4 contour levels, but is there a better way?
> 
> thanks,
> Esther
> ---
> Esther Bullitt, Ph.D.
> Dept. of Physiology & Biophysics
> Boston University School of Medicine
> 700 Albany Street, Room W302
> Boston, MA  02118-2526
> 
> Email:      bullitt at bu.edu
> Telephone:  617-638-5037
> Facsimile:  617-638-4041
> http://www.bumc.bu.edu/phys-biophys/faculty/bullitt
> 
> 
> _______________________________________________
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