[Chimera-users] Reading a data set from a text file

Elaine Meng meng at cgl.ucsf.edu
Thu Jun 14 10:45:03 PDT 2007

Hi Kyaw,
It all depends on the format of the data in the text file.  Many file  
formats are text files, but differ in what data they contain and how  
the data values are arranged.  Chimera reads several different  
formats of "volume data" such as electron density:

If you have or can generate one of those file types, you can just use  
"File... Open" in the main Chimera menu or "File... Open map" in the  
Volume Viewer menu to read the data from the file.  Volume Viewer is  
under "Tools.... Volume Data" in the Chimera menu.  Then, in Volume  
Viewer you can show isosurfaces, including mesh, of the data.

Here is a tour of volume data-related features:

some tutorials on the web:

and the full Volume Viewer documentation:

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jun 14, 2007, at 10:17 AM, Kyaw Zeyar Myint wrote:

> Hi,
> I am Kyaw Myint, a summer intern at NIAMS branch of NIH. I am working
> under the supervision of Dr. Bernard Heymann from the Lab of
> Structural Biology research.
> The project I am working on currently is to improve the 3D
> reconstruction of viruses' structures from 2D electron micrographs.
> The programs I am using include Chimera and Bsoft.
> For the project, I want to read in a data set from a text file and
> display the 3D surfaces based on that data set. I'd like to use
> Chimera for that purpose and I'd really appreciate any suggestion or
> comment on how I should do that. Thank you very much for your help in
> advance.
> Looking forward to hearing from you soon,
> Kyaw
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> Chimera-users at cgl.ucsf.edu
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