I am rendering a two-submit protein, split, with different colored mesh surfaces on the subunits. If I render to an image with Chimera, the surfaces appear in the colors assigned. If I render with POV-Ray, both mesh surfaces render as black. I assigned the colors using MSMS surface attributes with color sources as "atoms", using the color well in the Component Atom Attributes panel. Where in the literature should I read to sort this out? Thanks!
Hi Greg, This is not an answer to your question per se, just sharing my own perspective. (1) The Chimera export to POVray has many imperfections and even without the problem you describe, in my experience, the POVray result often looks dark and dingy. (2) I have much better success rendering with Chimera directly. It depends what effect you are trying to achieve, but you can turn on shadows (e.g. command "set shadows") and adjust the shininess directly in Chimera. Another big advantage is that WYSIWYG. See Chimera "Image Tips" for a list of image-related parameters and all the says in which you can change them. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#tips> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 15, 2020, at 10:33 AM, Greg Williams <gregoryw@comcast.net> wrote:
I am rendering a two-submit protein, split, with different colored mesh surfaces on the subunits. If I render to an image with Chimera, the surfaces appear in the colors assigned. If I render with POV-Ray, both mesh surfaces render as black. I assigned the colors using MSMS surface attributes with color sources as "atoms", using the color well in the Component Atom Attributes panel.
Where in the literature should I read to sort this out?
Thanks!
Hi Greg, I believe the problem is that the meshes are composed of lines, and the lines don't get lit properly by POVray, basically because they don't have normals. You would probably have better success with semi-transparent solid surfaces than mesh surfaces. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Nov 15, 2020, at 10:33 AM, Greg Williams <gregoryw@comcast.net> wrote:
I am rendering a two-submit protein, split, with different colored mesh surfaces on the subunits. If I render to an image with Chimera, the surfaces appear in the colors assigned. If I render with POV-Ray, both mesh surfaces render as black. I assigned the colors using MSMS surface attributes with color sources as "atoms", using the color well in the Component Atom Attributes panel.
Where in the literature should I read to sort this out?
Thanks!
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Or, you can make meshes into "molecules" (i.e. 3D sticks) using the "meshmol" command: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/meshmol.html> Still, I generally recommend direct rendering with Chimera over the povray export approach. Elaine
On Nov 17, 2020, at 11:49 AM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Greg, I believe the problem is that the meshes are composed of lines, and the lines don't get lit properly by POVray, basically because they don't have normals. You would probably have better success with semi-transparent solid surfaces than mesh surfaces.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Nov 15, 2020, at 10:33 AM, Greg Williams <gregoryw@comcast.net> wrote:
I am rendering a two-submit protein, split, with different colored mesh surfaces on the subunits. If I render to an image with Chimera, the surfaces appear in the colors assigned. If I render with POV-Ray, both mesh surfaces render as black. I assigned the colors using MSMS surface attributes with color sources as "atoms", using the color well in the Component Atom Attributes panel.
Where in the literature should I read to sort this out?
Thanks!
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Eric, export a surface mesh in the pov format and you'll see that the lines are converted to cylinders, so they are lit. There is a disconnect between POV-ray's lighting model and Chimera's lighting model, so the highlights are not the same. Maybe the meshes are shadowed? In that case moving the light source to be more of a headlight would help. -- Greg On 11/17/2020 11:49 AM, Eric Pettersen wrote:
Hi Greg, I believe the problem is that the meshes are composed of lines, and the lines don't get lit properly by POVray, basically because they don't have normals. You would probably have better success with semi-transparent solid surfaces than mesh surfaces.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Nov 15, 2020, at 10:33 AM, Greg Williams <gregoryw@comcast.net> wrote:
I am rendering a two-submit protein, split, with different colored mesh surfaces on the subunits. If I render to an image with Chimera, the surfaces appear in the colors assigned. If I render with POV-Ray, both mesh surfaces render as black. I assigned the colors using MSMS surface attributes with color sources as "atoms", using the color well in the Component Atom Attributes panel.
Where in the literature should I read to sort this out?
Thanks!
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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participants (4)
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Elaine Meng -
Eric Pettersen -
Greg Couch -
Greg Williams