Hi, I just updated my Chimera installation to 1.4.1 (Mac OSX aqua), and I noticed that for some reason shadows are not so nicely rendered in standard 3x3 super-sampled output. They look very blocky, much as they always have done in the viewer. In version 1.4 I always got very nice shadows when I saved an image. I am trying to save images of an isosurface view of a 3D reconstruction. Is there a setting I need to adjust to get high quality shadows back again? Many thanks, Dave Dr David Bhella MRC Virology Unit Church Street Glasgow G11 5JR Telephone: 0141-330-3685 Graphics lab: 0141-330-2989 Mobile: 07717-202439 Skype: d.bhella Virus Structure Web Site: http://www.mrcvu.gla.ac.uk/research/bhellad/virus_structure.htm Molecular Machines - Images from Virus Research (Art Exhibition): http://www.molecularmachines.org.uk Departmental Web Site: http://www.mrcvu.gla.ac.uk/staff/bhellad.html
Hi David, I'm a bit confused about what you mean. Images saved directly from Chimera (non-raytraced) do not have shadows per se, but they do have "shading." Although there is an "show shadows" setting in the Effects tool, it is turned off by default, and those shadows are always blocky as far as I know, and not intended for saved images, only as interactive previews for raytracing. You probably aren't using that "show shadows" setting. Conversely, with raytracing there is no such thing as supersampling. If you were showing atoms/ribbons, I'd suggest increasing "subdivision quality" (also in Effects) to increase the smoothness of the objects and thus the shading in Chimera. However, this does not affect isosurfaces. There are separate smoothing controls in Volume Viewer for such surfaces, see this recent post: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-February/004764.html
Check that you are using the full resolution of your data and not a subsampling (coarser grid). My only other idea is that maybe you were using raytracing before. If none of these comments help, please use "Help... Report a Bug" in the Chimera menu and include a complete description of your situation. This also allows attaching a file and including your email address for a response. Best, 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 Feb 12, 2010, at 8:06 AM, David Bhella wrote:
Hi, I just updated my Chimera installation to 1.4.1 (Mac OSX aqua), and I noticed that for some reason shadows are not so nicely rendered in standard 3x3 super-sampled output. They look very blocky, much as they always have done in the viewer. In version 1.4 I always got very nice shadows when I saved an image. I am trying to save images of an isosurface view of a 3D reconstruction. Is there a setting I need to adjust to get high quality shadows back again? Many thanks, Dave
Hi Elaine, Sorry for the confusion, yes I did have 'show shadows' enabled and in version 1.4 this gave really nice shadows for 3d reconstructions as well as molecular surfaces. So much so that I had stopped using POV-RAY altogether because of the time penalty when ray-tracing a long movie. One difference I noticed between 1.4 and 1.4.1 is that when rendering supersampled images in 1.4 there was no flashing of each tile in the viewer, rather it just said 'rendering high resolution image' at the bottom of the window. This may or may not relate to the manner in which the image is calculated (sorry if that seems a bit of a random observation!) D. Quoting Elaine Meng <meng@cgl.ucsf.edu>:
Hi David, I'm a bit confused about what you mean. Images saved directly from Chimera (non-raytraced) do not have shadows per se, but they do have "shading." Although there is an "show shadows" setting in the Effects tool, it is turned off by default, and those shadows are always blocky as far as I know, and not intended for saved images, only as interactive previews for raytracing. You probably aren't using that "show shadows" setting. Conversely, with raytracing there is no such thing as supersampling.
If you were showing atoms/ribbons, I'd suggest increasing "subdivision quality" (also in Effects) to increase the smoothness of the objects and thus the shading in Chimera. However, this does not affect isosurfaces. There are separate smoothing controls in Volume Viewer for such surfaces, see this recent post: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-February/004764.html >
Check that you are using the full resolution of your data and not a subsampling (coarser grid).
My only other idea is that maybe you were using raytracing before.
If none of these comments help, please use "Help... Report a Bug" in the Chimera menu and include a complete description of your situation. This also allows attaching a file and including your email address for a response. Best, 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 Feb 12, 2010, at 8:06 AM, David Bhella wrote:
Hi, I just updated my Chimera installation to 1.4.1 (Mac OSX aqua), and I noticed that for some reason shadows are not so nicely rendered in standard 3x3 super-sampled output. They look very blocky, much as they always have done in the viewer. In version 1.4 I always got very nice shadows when I saved an image. I am trying to save images of an isosurface view of a 3D reconstruction. Is there a setting I need to adjust to get high quality shadows back again? Many thanks, Dave
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I'm going to assume that you turned on shadows in the Effects tool. So we didn't intentionally make it worse. And we do plan to improve it, ticket #7892. Improving it has been on the back burner, because the shadow effect was implemented to preview where shadows would be if you raytraced the image, but I agree that it would be better if they were always better interactively. The quality of shadows in the current implementation varies tremendously depending on how big your window is (1024x1024 is better than 512x512), and which graphics driver you are using -- NVidia graphics drivers currently give better results. So I hope the results you are seeing are because you are using a smaller window or a different graphics driver. If not, please use chimera Help / Report a Bug dialog. Hope this helps, Greg P.S. I've taken the liberity to add you to the cc list on ticket #7892 so you'll be notified when the shadow code is improved. On Fri, 12 Feb 2010, David Bhella wrote:
Hi,
I just updated my Chimera installation to 1.4.1 (Mac OSX aqua), and I noticed that for some reason shadows are not so nicely rendered in standard 3x3 super-sampled output. They look very blocky, much as they always have done in the viewer. In version 1.4 I always got very nice shadows when I saved an image. I am trying to save images of an isosurface view of a 3D reconstruction. Is there a setting I need to adjust to get high quality shadows back again?
Many thanks,
Dave
participants (4)
-
David Bhella -
dbhel001＠udcf.gla.ac.uk -
Elaine Meng -
Greg Couch