[Chimera-users] How to fit an atomic model into a topographic height volume

Elaine Meng meng at cgl.ucsf.edu
Sat Aug 22 09:05:02 PDT 2020

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.


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 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 at 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>

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