Re: [PyMOL] change in VRML format output
Thomas, Thanks. I re-wrote my blender scripts to accommodate both version, since it seems like other visualization programs generally output bonds as two cylinders. What I would love, though I'm not even sure its possible with vrml2, would be export some 'additional' info (like chain, resnum) that each object was associated with. --p On 02/28/2017 12:29 PM, Thomas Holder wrote: > Hi Paul, > > Interesting observation. This change was not intentional, it's a side effect > of a very low level change in the geometry generation. We should be able to > optimize this for the next PyMOL release. > > Cheers, >Thomas > > On 24 Feb 2017, at 12:02, Paul Paukstelis wrote: > >> There seem to have been some changes in how the VRML2 output is done >> between 1.7.X and 1.8.X, though I can't find it documented in change logs. >> >> In 1.7.X, vrml2 output would convert sticks to cylinders that was >> dependent on color. If a bond were split into two colors, it would >> output as two cylinders, but if the bond were one color it would just be >> one longer cylinder. There was also the annoying property that no matter >> what settings you included, vrml2 would always put extra spheres at the >> ends of cylinders to make them smooth (even though they were inside atoms) >> >> In 1.8.X bond cylinders are always exported as two separate cylinders, >> even when everything is colored the same, but the annoying spheres at >> the end of bonds are gone (yay!). >> >> Unfortunately, it turns out that when working with blender scripts it >> was much easier to make everything one color so each bond was a single >> cylinder. I can use an older version, but I was wondering if there is >> perhaps a new setting I haven't seen yet that might let me revert this >> behavior. >> >> Thanks. -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] change in VRML format output
Hi Paul, Interesting observation. This change was not intentional, it's a side effect of a very low level change in the geometry generation. We should be able to optimize this for the next PyMOL release. Cheers, Thomas On 24 Feb 2017, at 12:02, Paul Paukstelis wrote: > There seem to have been some changes in how the VRML2 output is done > between 1.7.X and 1.8.X, though I can't find it documented in change logs. > > In 1.7.X, vrml2 output would convert sticks to cylinders that was > dependent on color. If a bond were split into two colors, it would > output as two cylinders, but if the bond were one color it would just be > one longer cylinder. There was also the annoying property that no matter > what settings you included, vrml2 would always put extra spheres at the > ends of cylinders to make them smooth (even though they were inside atoms) > > In 1.8.X bond cylinders are always exported as two separate cylinders, > even when everything is colored the same, but the annoying spheres at > the end of bonds are gone (yay!). > > Unfortunately, it turns out that when working with blender scripts it > was much easier to make everything one color so each bond was a single > cylinder. I can use an older version, but I was wondering if there is > perhaps a new setting I haven't seen yet that might let me revert this > behavior. > > Thanks. -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] change in VRML format output
There seem to have been some changes in how the VRML2 output is done between 1.7.X and 1.8.X, though I can't find it documented in change logs. In 1.7.X, vrml2 output would convert sticks to cylinders that was dependent on color. If a bond were split into two colors, it would output as two cylinders, but if the bond were one color it would just be one longer cylinder. There was also the annoying property that no matter what settings you included, vrml2 would always put extra spheres at the ends of cylinders to make them smooth (even though they were inside atoms) In 1.8.X bond cylinders are always exported as two separate cylinders, even when everything is colored the same, but the annoying spheres at the end of bonds are gone (yay!). Unfortunately, it turns out that when working with blender scripts it was much easier to make everything one color so each bond was a single cylinder. I can use an older version, but I was wondering if there is perhaps a new setting I haven't seen yet that might let me revert this behavior. Thanks. -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
