[Chimera-users] Color sub-region with marker

Tom Goddard goddard at sonic.net
Tue Nov 2 18:52:02 PDT 2010

Hi Xiaofeng,

   The Chimera Color Zone tool has lots of limitations as you've noticed.

   The jagged edges on the colored region when using color zone happen 
because the surface is made up of triangles and Chimera can only color 
each triangle vertex and then linearly interpolates colors across the 
triangle based on the 3 vertex values.  That can look bad.  Your 
solution of using the "subdivide surface" option in the volume dialog 
surface surface and mesh options panel will help reduce the jaggedness.  
There is one tricky solution that can produce a smoother edge.  It uses 
a command I just added a month ago called "measure contactarea".  The 
virtue of this approach is that it creates a new surface chopping the 
triangles at the edge of your zone to make a perfect smooth boundary.  
But it wasn't intended as a substitute for the color zone dialog.  
Instead it measures the area on one surface within a given distance of 
another surface and displays that contact area.  The first problem using 
this is that it doesn't use markers and a surface like color zone -- 
instead it uses two surfaces.  So the first trick is to turn your 
markers into a surface.  If the markers are model #1 use

     molmap #1 3

to make a 3 Angstrom resolution surfaces for those markers.  Now to 
color a zone around those markers on volume data #0 use

     measure contactarea #0 #1 12 color tan

This will make a new surface matching volume surface #0 within a range 
of 12 Angstroms from surface #1 (the marker surface created with 
molmap).  It has beautiful smooth edges.  See the attached picture.  
You'll need a Chimera daily build to use "measure contactarea".  I 
suggest tonight's daily build, because I made some changes to "measure 
contactarea" to make the surface look very smooth.  Earlier daily builds 
had a less smooth edge, and less smooth colored region.  If you add 
"slab 2" as an option it will make the colored patch have thickness 2A 
(not shown).

   1) You can't use different color zone radii on the same surface at 
the same time.  This is item 37 in the Chimera feature request list.


You can use the above trick multiple times to create color patches using 
different radii.

   2) Not sure I understand this question.  I think you are asking if 
you can color inside rectangles and ellipses.  There's no way to do that 
now.  I'm not sure how you would describe the rectangle or ellipse with 
a marker since a marker is a sphere and those shapes have non-equivalent 
axes.  You can create such shapes with the Chimera "shape" command but 
you can't for instance color everything within such a shape.  The 
closest you can do is color near a traced path made with markers and 
links.  This basically lets you color in a cylindrical zone.  To enable 
this you use the bondzone command


   3) Not sure exactly what case you are interested in.  If you clip a 
surface you can place markers exactly of the "cap" surface that covers 
the hole left by clipping.  You would use the Volume Tracer mouse mode 
with "Place markers on surfaces" enabled.  If you wanted to place 
markers on single data planes of a volume you would enable "Place 
markers on data planes".


> Dear Chimera users,
> I always have problems when I color a sub-region of density map by markers. Rather than a zigzag, boundary, I try to create a smooth curve boundary of sub-region from a whole density 3D volume. In this case, if I just put one marker and select a big coloring radius, the boundary in cross-view will show a circle curve at the boundary, however if I use a very small coloring radius and put more and closer markers on the boundary, the boundary shows a sawtooth in cross-view, even I choose 4 times for subdividing surface. Or is there any other way to do this instead of markers? And I have several other questions:
> (1) Is that possible to have different coloring radius in one Chimera session?
> (2) except for ball shape, can we have more options on the coloring object with markers? For example rectangular, ellipse and so on.
> (3) Is that possible to put markers directly on the clip planes?
> Thanks in advance,
> Xiaofeng

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