Hi, I am trying to render an image that includes a difference map density displayed as a solid object. When I try to get the image directly from the screen it shows patterns of pixelation. I then tried POVRAY and the solid object data does not show up. Is there anything that I am missing? Thanks -- +---------------------------------+ | Mario J. Borgnia, Ph. D. | | | | Lab of Cell Biology | | NIH NCI/CCR | | 50 South Drive Rm 4306 MSC 8008 | | Bethesda MD 20892-8008 | | | | Tel: (301) 594 0563 | | mborgnia@nih.gov | +---------------------------------+
Hi Mario, This is a limitation. The solid style volume display is not exported by Chimera to povray. I think povray supports volumetric rendering http://local.wasp.uwa.edu.au/~pbourke/miscellaneous/df3/ but we do not export the needed data. I don't know if povray would be able to lessen the pixelation artifacts. They come from the volume data voxel size. You could minimize those artifacts by resampling your volume on a finer grid, displaying in Chimera, and using the non-povray Chimera image save. Here is some info about how to do that resampling in Chimera http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#resampl... Those instructions talk about resampling on a rotated grid, but you can just leave the grid unrotated. Tom
Hi,
I am trying to render an image that includes a difference map density displayed as a solid object. When I try to get the image directly from the screen it shows patterns of pixelation. I then tried POVRAY and the solid object data does not show up. Is there anything that I am missing?
Thanks
FYI, if you haven't done it already, the simplest way to resample your volume to a higher resolution is to change the step size in the step menu to 1. - Greg On 06/16/2010 10:39 AM, Tom Goddard wrote:
Hi Mario,
This is a limitation. The solid style volume display is not exported by Chimera to povray. I think povray supports volumetric rendering
http://local.wasp.uwa.edu.au/~pbourke/miscellaneous/df3/
but we do not export the needed data.
I don't know if povray would be able to lessen the pixelation artifacts. They come from the volume data voxel size. You could minimize those artifacts by resampling your volume on a finer grid, displaying in Chimera, and using the non-povray Chimera image save. Here is some info about how to do that resampling in Chimera
http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#resampl...
Those instructions talk about resampling on a rotated grid, but you can just leave the grid unrotated.
Tom
Hi,
I am trying to render an image that includes a difference map density displayed as a solid object. When I try to get the image directly from the screen it shows patterns of pixelation. I then tried POVRAY and the solid object data does not show up. Is there anything that I am missing?
Thanks
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Hi Mario, No, you're not missing anything: one of the limitations of raytracing is that it does not handle solid volume displays. Raytracing limitations are listed at the bottom of this page: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/raytracing.html> Perhaps there are some Volume Viewer settings or data filtering that can improve the appearance in Chimera. In Volume Viewer, use the Features menu to show "solid rendering options". There is also a Volume Filter tool with various smoothing capabilities. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#dispsolid> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/gaussian.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jun 16, 2010, at 10:31 AM, Mario J. Borgnia wrote:
Hi, I am trying to render an image that includes a difference map density displayed as a solid object. When I try to get the image directly from the screen it shows patterns of pixelation. I then tried POVRAY and the solid object data does not show up. Is there anything that I am missing? Thanks
participants (4)
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Elaine Meng -
Greg Couch -
Mario J. Borgnia -
Tom Goddard