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

Thomas Goddard goddard at cgl.ucsf.edu
Tue Jul 17 12:11:43 PDT 2007

Hi Kyaw,

   I see what you've done and see that you have a set of (x,y,z) 
coordinates.  But I'm not sure what you want or what these coordinates 

   To make a surface out of a set of points you need to know which 
points are next to each other.  In Chimera you need a set of points, and 
a set of triangles, each triangle defined by 3 integer indices into the 
set of points that give the triangle vertices.  If you can define the 
set of triangles I can tell you how to make the surface.


Kyaw Zeyar Myint wrote:
> Hello Tom,
>         I apologize for not being able to respond to you earlier. The 
> set of view vectors that I want to make surface out of it are in (x, y, 
> z) coordinates.
> So far, I've done a quick and 'rough' way of using these vectors for 
> display. What I did in chimera was that I wrote a mini plugin which 
> makes a .bild 
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html> file with a 
> set of cylinders, given a set of vectors. 
>        Each cylinder is centered at origin (0,0,0) and drawn according 
> to the vector (which is from my set of view vectors). So if the V(x,y,z) 
> has (0.0523, 0.0000, 0.9986), then the cylinder is drawn by:   
>  /.cylinder 0 0 0 0.0523 0.0000 0.9986 0.03 /    in .bild file.
>        Then .bild file is fed into chimera and then a set of cylinders 
> is displayed. In a sense, each cylinder represents each view vector in 
> the set. But this is just a quick solution. 
>         If you can share some ideas of how to better do this, please let 
> me know. I'd really appreciate your help.
> Thanks a lot!
> Kyaw
> (P.S: I've attached .bild file which you can display in chimera and see 
> what inside using a text editor.)
> ------------------------------------------------------------------------
> On Jun 29, 2007, at 1:03 PM, Tom Goddard wrote:
>> Hi Kyaw,
>>  I'm not sure I understand what type of data you want to display in 
>> Chimera.  Is it a list of density values, or is it a list of x, y, and 
>> z coordinates?  If it is density values in text rather than binary, 
>> you could reformat it into XPLOR format
>>    http://www.scripps.edu/rc/softwaredocs/msi/xplor981/formats.html
>> which can be read into Chimera.
>>    Tom

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