[Chimera-users] Color sub-region with marker

Tom Goddard goddard at sonic.net
Wed Nov 3 17:00:37 PDT 2010

Hi Xiaofeng,

   That makes sense.  The surface cap (i.e. the flat surface that covers 
a hole in the surface when clipping) is a second surface piece.  I plan 
on making "measure contactarea" handle multiple surface pieces but have 
not gotten to it yet.


> It works right now, I find that It won't work if surface capping is on.
> Xiaofeng
> ----- Original Message -----
> Hi Xiaofeng,
>     The Chimera daily build with the outline box fix is not available
> yet.  You can simply turn off the outline box in the volume dialog Data
> Display Options panel.
>     The Chimera daily builds are made automatically starting at 9 pm
> Pacific time and then put on the download web page if they succeed,
> usually after midnight.  The builds don't always work, so check the date
> on the download page for the build you want -- you'll need Nov 4 for the
> outline box fix.
>       Tom
>> Hi Tom,
>> The second problem was clear to me.
>> Have you already uploaded tonight's Chimera build?
>> Thanks,
>> Xiaofeng
>> ----- Original Message -----
>> Hi Xiaofeng,
>>      I fixed "measure contactarea" so it will ignore outline boxes in
>> tonight's Chimera builds.
>>        Tom
>>> 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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