[Chimera-users] Color sub-region with marker

Tom Goddard goddard at sonic.net
Wed Nov 3 16:15:09 PDT 2010

Hi Xiaofeng,

   I fixed "measure contactarea" so it will ignore outline boxes in 
tonight's Chimera builds.


> Hi Xiaofeng,
>     The measure contactarea command can only handle surfaces consisting
> of a single surface pieces.  Surfaces can have more than one selectable
> piece, but molmap makes a single piece surface so I'm puzzled by the
> error you get.  I see that if you have an outline box shown for the
> molmap surface then that is considered a second surface piece and will
> generate the error message you see.
>     For your second problem, I can put markers on the clipping surface
> cap using "place markers on surface" but the trouble is the markers are
> clipped so you don't see them.  The near/far clipping planes clip
> everything.  You do see half of a spherical marker (clipped in half) if
> you hide the map after placing the marker on the clip surface.  I'd
> suggest using Per-Model Clipping (menu Tools / Depiction) to clip just
> the map surface -- that way you will be able to see the markers you
> place on the clip plane.
>       Tom
>> Hi Tom,
>> Thanks for your reply. The questions are:
>> (1) When I follow your procedure until "measure contactarea #0 #1 12 color tan", it promotes "#0 has 2 surface pieces, require1" and stop working. I don't understand what that means(figure attached).
>> (2) The question of number 3 at last time about how to put markers directly on the clipped plane is that, for example, in Side view window, when I move the front bar (normally the front and behind bar just cover the object) into the object to observe inside, I try to put markers on this capped plane inside the object, but it doesn't work even I have chosen "put markers on surface".
>> Xiaofeng
>> ----- Original Message -----
>> 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.
>>        http://plato.cgl.ucsf.edu/trac/chimera/wiki/requests
>> 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
>>        http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/bondzone.html
>>      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".
>>        Tom
>>> 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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