On Sun, Apr 25, 2010 at 2:22 AM, Wayne Decatur <wdeca...@yahoo.com> wrote:
> Now that Proteopedia can run the signed applet (using a technique where you > can load the page with a custom version of Jmol) I have been trying the > different image outputs and come across some issues and hopes: > > a) The current output of Jmol to VRML seems to have a problem around line > 29 where the line beginning 'reset;center...' is not commented out and so > causes nothing to load (in SwirlX3D viewer) or throws an error message about > line 29 (vrml2pov converter). Either commenting out that line or hitting > backspace to keep it running on with the line above allows both programs to > work. > I'm not seeing "reset" in any of the VRML files I've created with Jmol. What's that about? Line 29 of the VRML output from Jmol? I'm not seeing the point of converting Jmol to VRML to POV-Ray. Why not just create the POV-Ray directly from Jmol? See http://chemapps.stolaf.edu/jmol/docs/examples-11/img/pov-test.png Jmol is definitely setting normals.... Bob > > b) Using VRML to convert to POV-Ray gives a high quality image (see , > http://drop.io/85qrkhy/asset/1rpu-vrml-to-povray-jpg for example) except > that regions of non-structured protein (loops) don't look smooth and nice > like the rest of the image. Can this be fixed or improved somehow > eventually? I looked at it directly in VRML and there it doesn't look good > either. Using either means of rendering it looks like the loops consists of > tiny multiple circles adjacent one another. The nucleic acid backbone looks > beautifully very smooth though. Playing with lighting effects can produce > even better results from Jmol via this route but the loops still detract. > (Example of VRML to POV result with lighting effects added > http://drop.io/85qrkhy/asset/1rpu-light-efffects-jpg . I think though I > put the light in the wrong position in a cut and paste from another scene > and got artifacts; however, it takes about an hour to render so I left it.) > > > circles would be an indication you aren't using set hermiteLevel 5 > c) I am going from VRML to POV because the current implementation of > Jmol's generated POV-Ray files does not create surface normals like > Swiss-PDB Viewer does with smooth_triangles and Pymol does with a mesh2 > objects. > I think you are just forgeting to use hermiteLevel. > And thus it does not render a high quality image (see > http://drop.io/85qrkhy/asset/1rpufromjmol-pov-jpg , for an example of the > POV-Ray rendering as straight from Jmol)? In fact the Jmol image using > Proteopedia's high quality toggle is much better, and unlike the files that > come straight out of Pymol or Swiss-PDV viewer the objects are not suitable > for being taken and used in advanced scenes that use fancy lighting effects > or that have objects that do render at a very high resolution. The VRML > output seems to contain the normals? Can the normals be generated by Jmol in > its POV-Ray out so people can use that without needing the VRML to POV-Ray > step (although I am not 100% sure the VRML output has it as I don't know > VRML). > All the normals are there for POV-ray. I think you just are being caught by the fact that the VRML automatically sets hermiteLevel to 5, and POV-ray doesn't. That's on purpose. The idea in the POV-ray was to recreate EXACTLY the image in Jmol; the idea in VRML is to have a 3D object. In a sense, without hermiteLevel, the POV-ray is only a 2D (paper-thin) object embedded in 3D. > More importantly, I think it would also make the POV-Ray output look better > especially for people trying to make the rendering larger (although I had a > hard time myself adjusting the height and width with Jmol's output to get a > larger rendering where as I find it easily done with the output generated by > Swiss PDB-viewer). > > Thanks, > Wayne > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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