Hi,
I image an .mrc map in Chimera. The surface map is displayed using a selected range. As a result I see blobs.
I want to be able to select such a blob and get back its 3d information - coordinates, etc...
Would it be possible to implement this feature?
Greetings,
Tatiana
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Tatiana Gorelik, PhD,
Institut für Physikalische Chemie
Johannes Gutenberg-Universität Mainz
Welderweg 11
55099 Mainz
Germany
Tel.: 0049 6131 39 22347
Fax: 0049 6131 39 23768
e-mail:gorelik@uni-mainz.de
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Hi Tatiana,
If you want the (x,y,z) coordinates for the a connected piece of a contour surface you could use the "Color and Measure Surface Pieces" extension on the Chimera experimental features page (2nd from the bottom):
http://www.cgl.ucsf.edu/chimera/experimental/experimental.html
http://www.cgl.ucsf.edu/chimera/experimental/pickblobs/pickblobs.html
That extension allows you to colors and reports the volume and area of individual blobs chosen with the mouse. You could add a small bit of Python code to that extension to print the surface coordinates. For example, you could add
for xyz in varray: print '%12.5f %12.5f %12.5f' % xyz
at the end of the color_and_measure() routine in PickBlobs/gui.py to print the blob surface vertex coordinates. The printed results would go to the Chimera Reply Log dialog when you click on a blob. Those coordinates could be saved to a file (cut and paste). The triangles that make up the surface blob are described by tarray (N by 3) where each triple of integers defines the indices of the triangle vertices in varray.
Tom
participants (2)
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Gorelik, Tatiana
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Tom Goddard