Extension to export VTK format files
Hello all, As part of a project that I am working on, I recently wrote an extension for Chimera that exports the scene as a .vtk file which can be read into the Visualization Toolkit <http://www.vtk.org> or Paraview<http://www.paraview.org>. It exports atoms (points), bonds (lines) and surfaces along with other data associated with them such as the atom and residue names, residue number, position along its chain, b-factor, occupancy, etc. in a format that can be used in VTK-based applications with the default file readers. I think this could be a good thing to add to Chimera itself, so I was wondering if you would like to have the code for the extension to add to Chimera itself. I look forward to hearing from you, -- Shawn Waldon Graduate Research Assistant Department of Computer Science University of North Carolina at Chapel Hill swaldon@cs.unc.edu
Hi Shawn, That is interesting. We could put it in Chimera if the code is solid. The error reports will come to us so we need high quality code so we have time to do more than reply to bug reports. What use of molecules in VTK motivated you to write this export code? Tom On Jul 16, 2013, at 11:30 AM, Shawn Waldon wrote:
Hello all,
As part of a project that I am working on, I recently wrote an extension for Chimera that exports the scene as a .vtk file which can be read into the Visualization Toolkit or Paraview. It exports atoms (points), bonds (lines) and surfaces along with other data associated with them such as the atom and residue names, residue number, position along its chain, b-factor, occupancy, etc. in a format that can be used in VTK-based applications with the default file readers. I think this could be a good thing to add to Chimera itself, so I was wondering if you would like to have the code for the extension to add to Chimera itself.
I look forward to hearing from you, -- Shawn Waldon Graduate Research Assistant Department of Computer Science University of North Carolina at Chapel Hill swaldon@cs.unc.edu _______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev
Hi Tom, I don't know exactly how high quality it is. I haven't found any bugs in my latest version, but that doesn't mean they aren't there. I am fairly new to python, so there may be some subtleties that I missed. Also, do you have coding conventions listed somewhere? I have looked, but I haven't found an official list or anything. I am willing to fix it up a bit before submitting it if you can point me to a list of things to fix up. My use case is that I am writing a higher level modeling tool that uses VTK to do its graphics. I have been calling Chimera as a subprocess to get a surface to render (and now other data). See the project website for more details: http://www.sketchbio.org Shawn On Tue, Jul 16, 2013 at 10:49 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Shawn,
That is interesting. We could put it in Chimera if the code is solid. The error reports will come to us so we need high quality code so we have time to do more than reply to bug reports.
What use of molecules in VTK motivated you to write this export code?
Tom
On Jul 16, 2013, at 11:30 AM, Shawn Waldon wrote:
Hello all,
As part of a project that I am working on, I recently wrote an extension for Chimera that exports the scene as a .vtk file which can be read into the Visualization Toolkit <http://www.vtk.org> or Paraview<http://www.paraview.org>. It exports atoms (points), bonds (lines) and surfaces along with other data associated with them such as the atom and residue names, residue number, position along its chain, b-factor, occupancy, etc. in a format that can be used in VTK-based applications with the default file readers. I think this could be a good thing to add to Chimera itself, so I was wondering if you would like to have the code for the extension to add to Chimera itself.
I look forward to hearing from you, -- Shawn Waldon Graduate Research Assistant Department of Computer Science University of North Carolina at Chapel Hill swaldon@cs.unc.edu
_______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev
-- Shawn Waldon Graduate Research Assistant Department of Computer Science University of North Carolina at Chapel Hill swaldon@cs.unc.edu
Hi Shawn, The SketchBio project looks cool. We are trying to make it easy to build hypothetical models of hiv, muscle sarcomeres, fibronectin and all manner of large molecular machinery in Chimera. It is a difficult user interface problem. Graham Johnson, Sam Hertig and I are trying to move this project along. We are happy to help your efforts on this problem. Can you send us your Chimera VTK export code and I'll take a look. We don't have a list of coding conventions. I don't really care how you indent your lines, or capitalize your variable names. Mostly I want the user to know when an error occurs what the nature of the problem is (e.g. export can't handle surfaces) without having to ask us. Tom On Jul 25, 2013, at 1:32 PM, Shawn Waldon wrote:
Hi Tom,
I don't know exactly how high quality it is. I haven't found any bugs in my latest version, but that doesn't mean they aren't there. I am fairly new to python, so there may be some subtleties that I missed. Also, do you have coding conventions listed somewhere? I have looked, but I haven't found an official list or anything. I am willing to fix it up a bit before submitting it if you can point me to a list of things to fix up.
My use case is that I am writing a higher level modeling tool that uses VTK to do its graphics. I have been calling Chimera as a subprocess to get a surface to render (and now other data). See the project website for more details: http://www.sketchbio.org
Shawn
On Tue, Jul 16, 2013 at 10:49 PM, Tom Goddard <goddard@sonic.net> wrote: Hi Shawn,
That is interesting. We could put it in Chimera if the code is solid. The error reports will come to us so we need high quality code so we have time to do more than reply to bug reports.
What use of molecules in VTK motivated you to write this export code?
Tom
On Jul 16, 2013, at 11:30 AM, Shawn Waldon wrote:
Hello all,
As part of a project that I am working on, I recently wrote an extension for Chimera that exports the scene as a .vtk file which can be read into the Visualization Toolkit or Paraview. It exports atoms (points), bonds (lines) and surfaces along with other data associated with them such as the atom and residue names, residue number, position along its chain, b-factor, occupancy, etc. in a format that can be used in VTK-based applications with the default file readers. I think this could be a good thing to add to Chimera itself, so I was wondering if you would like to have the code for the extension to add to Chimera itself.
I look forward to hearing from you, -- Shawn Waldon Graduate Research Assistant Department of Computer Science University of North Carolina at Chapel Hill swaldon@cs.unc.edu _______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev
-- Shawn Waldon Graduate Research Assistant Department of Computer Science University of North Carolina at Chapel Hill swaldon@cs.unc.edu
participants (2)
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Shawn Waldon -
Tom Goddard