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@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@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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, Kyaw 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@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@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users