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 represent. 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. Tom 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.)
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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
if you don't have connectivity defined already (your set of triangles), I think VTK (and other free packages out there) will derive the connectivity for you, if you assume that all points lie on the surface - (Delaunay tessellation/triangulation). Matlab also has this, if you have access. These algorithms will often give you back the points with a convention defining the surface normal, which may be important. -Jeff Quoting Thomas Goddard <goddard@cgl.ucsf.edu>:
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 represent.
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.
Tom
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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