[Chimera-users] Area central hole oligomer

Tom Goddard goddard at sonic.net
Sat Apr 13 10:11:14 PDT 2019

Another way to measure hole crosssectional area would be to multiply the map by -1 (vop scale #0 factor 1) so surfaces now surround low density instead of high density, then show just one plane cutting through the hole using Volume Viewer menu Features / Region Bounds, then use the Measure and Color Blobs tool to click on the hole surface and report its area.  Note the value reported is twice the hole area since the single plane surface is really 2 planar surfaces facing in opposite directions.


> On Apr 13, 2019, at 8:30 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Roberto,
> There isn’t a tool to do it in a single step, but you could try using Volume Tracer to add several markers around the hole when viewing your data as a plane, and then create a polygonal surface from those markers, then measure the area of that surface.  See "Markers: Creation" and "Surface Creation” in the Volume Tracer documentation:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/framevolpath.html>
> Example shown in attached picture:
> I opened EMDB 1024 and showed a single plane as surfaces in Volume Viewer (you can use its menu: Feature…Planes).  I started Volume Tracer from the Tools menu.  In Volume Tracer: in Mouse menu I chose to place markers on data planes and link new marker and then added several markers.  Then to add link between first and last markers, in Mouse menu I chose to link consecutively selected markers and chose those two.  (If you mess up you can select a marker and use the Actions menu in Volume Tracer to delete it.)  Now I had a closed loop of linked markers.  Then in Volume Tracer, Features menu I chose Surface and then clicked the surface “Create” button (after clearing selection so that no markers were selected).  Then in Model Panel you can see surface is #2, so I used command “measure area #2” which reports surface are in the status line and Reply Log.
> There was a hole but you can’t see it in the picture because the yellow surface is covering it.
> This workflow is for an X, Y, or Z plane.  If the hole axis is not aligned with data axes, then instead of using this planes approach you might have to show the full box but then use per-model clipping to slice at an angle.  I did not try that.
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> <Screen Shot 2019-04-13 at 8.18.24 AM.png>
>> On Apr 12, 2019, at 11:34 PM, Roberto Marotta <Roberto.Marotta at iit.it> wrote:
>> Hi,
>> I have the density map of a large oligomer resolved at 5 A.  I would like to measure the area of the hole  at the center of the oligomer. The five subunits that form the oligomer delimit the hole that is open and irregular in shape.
>> My idea is to measure the area of the hole in a central slice of the map.
>> Amy suggestions are really appreciated!
>> Thank you,
>> Roberto
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