Hello, It would be absolutely great if ChimeraX supported exporting to a VTK file like Chimera did. Are there any plans to port the VTK export functionality from Chimera to ChimeraX? If not, please consider doing it. Thank you very much. Sincerely, Angelos Angelopoulos
Hi Angelos, Ok, I ported the Chimera VTK exporter to ChimeraX, will be in tomorrow's ChimeraX builds. That code was originally contributed by Shawn Waldon as part of the SketchBio project in 2013. It exports to an ascii legacy VTK file data for only molecular structures and surfaces (not density maps). For molecular structures it exports points and lines for the atoms and bonds, and for surfaces it exports a mesh. At each point (atoms and surface) it exports attributes of the associated atom: modelNum, atomNum, resType, resNum, atomType, bFactor, occupancy, chainPosition. The modelNum, atomNum, resNum are integer indices (0 based). The models are numbered 0,1,2... sequentially (it does not use the model id from chimerax). The atom and residue numbers are the position in the list of atoms and residues for the entire structure they belong to. atomType and resType are what ChimeraX calls the atom name and residue name, e.g. CA and TRP. chainPosition is the residue index divided by the number of residues within the chain that the atom belongs to. I used the ParaView 5.8.0 viewer to check the exported VTK including the atom attributes. Tom
On Mar 18, 2020, at 5:36 PM, Angelos Angelopoulos <aangelos28@gmail.com> wrote:
Hello,
It would be absolutely great if ChimeraX supported exporting to a VTK file like Chimera did. Are there any plans to port the VTK export functionality from Chimera to ChimeraX? If not, please consider doing it.
Thank you very much.
Sincerely, Angelos Angelopoulos _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Tom, Thank you very much for porting it. I will try it out as soon as possible. Sincerely, Angelos Angelopoulos On Thu, Mar 19, 2020 at 6:51 PM Tom Goddard <goddard@sonic.net> wrote:
Hi Angelos,
Ok, I ported the Chimera VTK exporter to ChimeraX, will be in tomorrow's ChimeraX builds. That code was originally contributed by Shawn Waldon as part of the SketchBio project in 2013. It exports to an ascii legacy VTK file data for only molecular structures and surfaces (not density maps). For molecular structures it exports points and lines for the atoms and bonds, and for surfaces it exports a mesh. At each point (atoms and surface) it exports attributes of the associated atom: modelNum, atomNum, resType, resNum, atomType, bFactor, occupancy, chainPosition. The modelNum, atomNum, resNum are integer indices (0 based). The models are numbered 0,1,2... sequentially (it does not use the model id from chimerax). The atom and residue numbers are the position in the list of atoms and residues for the entire structure they belong to. atomType and resType are what ChimeraX calls the atom name and residue name, e.g. CA and TRP. chainPosition is the residue index divided by the number of residues within the chain that the atom belongs to.
I used the ParaView 5.8.0 viewer to check the exported VTK including the atom attributes.
Tom
On Mar 18, 2020, at 5:36 PM, Angelos Angelopoulos <aangelos28@gmail.com> wrote:
Hello,
It would be absolutely great if ChimeraX supported exporting to a VTK file like Chimera did. Are there any plans to port the VTK export functionality from Chimera to ChimeraX? If not, please consider doing it.
Thank you very much.
Sincerely, Angelos Angelopoulos _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (2)
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Angelos Angelopoulos -
Tom Goddard