How to fit an atomic model into a topographic height volume
Dear Chimera developers, I am a research fellow who works at Frederick Biophysics Laboratory and working on an image processing project. I used Chimera to generate a topographic height volume data from a single plane image. You can find the attached file and use a command following to generate the topographic surface. % topography #0 height -40 smoothingIteration 5 But there is no option for me to fit the atomic model into the surface height volume by using Fit in Map tools.
Can someone help me figure out what’s the issue? Is that possible to fit an atomic model into a height volume created by a single plane image or just simply need multiple planes? Thanks in advance.
Best, Yun-Tzai
Dear Yun-Tzai, The topographic surface from the "topography" command is a surface model, not a volume model, and you cannot fit into a surface model.
http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/topography.html
The fitting process is inherently 3D so I suspect that a single-plane volume is not enough information (2D only). However, I could not verify this without an example, and could not use your session because it does not include the volume data. You would need to supply both the session and the volume data file.
I have seen images such as from AFM with a molecule structure superimposed. However, it might require positioning the molecule by hand rather than using any automated tool.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 22, 2020, at 7:14 AM, Lee, Yun-Tzai (NIH/NCI) [F] yun-tzai.lee@nih.gov wrote:
Dear Chimera developers, I am a research fellow who works at Frederick Biophysics Laboratory and working on an image processing project. I used Chimera to generate a topographic height volume data from a single plane image. You can find the attached file and use a command following to generate the topographic surface. % topography #0 height -40 smoothingIteration 5 But there is no option for me to fit the atomic model into the surface height volume by using Fit in Map tools.
Can someone help me figure out what’s the issue? Is that possible to fit an atomic model into a height volume created by a single plane image or just simply need multiple planes? Thanks in advance.
Best, Yun-Tzai
<test.py>
Hi Yun-Tzai,
As Elaine said, there is nothing in Chimera to try to rotationally fit an atomic model into a height map represented as a surface or as a single plane volume with height values. That is a really exotic fitting problem. It is not even fitting an atomic model inside an enclosed surface since you just have the height, basically the profile on one face of the molecule, the upward face is this is atomic force microscopy data. I'd be surprised if there is any software in the world that does that. An algorithm might work by rotating the atomic model to 10000 different orientations, compute the height map in that orientation, then do a cross-correlation fit in 2D to the experimental 2D height map and take the orientation that produces highest correlation.
Tom
On Aug 22, 2020, at 7:14 AM, Lee, Yun-Tzai (NIH/NCI) [F] yun-tzai.lee@nih.gov wrote:
Dear Chimera developers, I am a research fellow who works at Frederick Biophysics Laboratory and working on an image processing project. I used Chimera to generate a topographic height volume data from a single plane image. You can find the attached file and use a command following to generate the topographic surface. % topography #0 height -40 smoothingIteration 5 But there is no option for me to fit the atomic model into the surface height volume by using Fit in Maptools.
Can someone help me figure out what’s the issue? Is that possible to fit an atomic model into a height volume created by a single plane image or just simply need multiple planes? Thanks in advance.
Best, Yun-Tzai
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participants (3)
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Elaine Meng -
Lee, Yun-Tzai (NIH/NCI) [F] -
Tom Goddard