[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
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:
> 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
> 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:
>> 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
>> Looking forward to hearing from you soon,
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
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