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

Kyaw Zeyar Myint myintk at mail.nih.gov
Thu Jun 14 11:53:31 PDT 2007

Hi Dr. Meng,

I am sorry for my vague question.

I have a table of numbers in a text file and I'd like to read in  
those numbers and convert them into cartesian coordinates so that  
they can be displayed as a surface in Chimera.

If you could give me some suggestions on how to do it, I'd really  
appreciate it.

Thank you,

On Jun 14, 2007, at 1:45 PM, Elaine Meng wrote:

> 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:
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume
> 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:
> http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html
> some tutorials on the web:
> http://www.cgl.ucsf.edu/chimera/tutorials/tutorials.html
> and the full Volume Viewer documentation:
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ 
> volumeviewer/framevolumeviewer.html
> I hope this helps,
> Elaine
> -----
> 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
>                      http://www.cgl.ucsf.edu/home/meng/index.html
> 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
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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