[Chimera-users] Reading a data set from a text file
triffo at rice.edu
triffo at rice.edu
Tue Jul 17 16:18:55 PDT 2007
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.
Quoting Thomas Goddard <goddard at 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
> 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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