[PyMOL] Export to COLLADA format
Hi all - I'm working on generating some interactive 3D figures, and have found that PyMOL is able to write .obj and .wrl files, which is nice. However, I would like to be able to use COLLADA (.dae) format. I have found tools (MeshLab and Blender, for example) that can convert among various formats, but the process is somewhat convoluted and tedious, and so far I've been unable to replicate the lighting, view, and scale of the PyMOL session in the resulting scene entirely, and certainly not without without a lot of manual adjustment in these programs. I don't know much about the internal data structures in PyMOL, but I wonder how complicated it would be to write a direct COLLADA exporter into PyMOL's save command (e.g. `save my_scene.dae`). There is a module called pycollada that seems to be fairly well documented and might be useful. In the meantime, I'd be interested in hearing about other solutions any of you may have worked out for converting .wrl files to .dae format, especially those that can be automated. Thanks in advance. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center 550 First Ave MSB 398 New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d___ 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] setting the cutoff radius that determines when atoms are bonded
Not sure what I was doing wrong before, but that worked like a charm! Thanks. Also, pyMol is really sweet. I've been bugging my group to use it for a few days now. :D Cheers, Rye On Tue, Dec 4, 2012 at 11:40 AM, Jason Vertrees < jason.vertr...@schrodinger.com> wrote: > Hi Rye, > > set connect_cutoff, 0.5 > > load 1.xyz > > produces different bonding than if you left the connect_cutoff value > to its default, 0.35. Set it to 0.85 and then load the file and you'll > see the Unknown atoms in the middle bonded as well. > > Cheers, > > -- Jason > > On Tue, Dec 4, 2012 at 11:33 AM, Rye Terrell > wrote: > > > > Hi Jason, > > > > Thanks for the tip. I still couldn't get it to work. I'll google around > some > > more, but here's the file. Thanks for any help. > > > > Cheers, > > Rye > > > > > > On Mon, Dec 3, 2012 at 4:34 PM, Jason Vertrees > > wrote: > >> > >> Hi Rye, > >> > >> How about connect_cutoff in Å? There's also connect_mode > >> (http://www.pymolwiki.org/index.php/Connect_mode). > >> > >> If you send me a copy of your file I can look at it. > >> > >> Cheers, > >> > >> -- Jason > >> > >> On Mon, Dec 3, 2012 at 4:03 PM, Rye Terrell > >> wrote: > >> > I have a silicon bulk system. Pymol indicates that a handful of the > >> > atoms > >> > are bonded to each other. Many bonds are not indicated. Is there some > >> > value > >> > I can adjust that will make pymol indicate that more atoms are > bonded? I > >> > usually do this by setting some cutoff radius, but googling around has > >> > yielded no results. I see that there is a way to bond atom pairs > >> > manually, > >> > but that would be incredibly tedious given the number of bonds there > >> > should > >> > be. > >> > > >> > Thanks for any help! > >> > Rye > >> > > >> > > >> > > -- > >> > Keep yourself connected to Go Parallel: > >> > BUILD Helping you discover the best ways to construct your parallel > >> > projects. > >> > http://goparallel.sourceforge.net > >> > ___ > >> > 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 > >> > >> > >> > >> -- > >> Jason Vertrees, PhD > >> Director of Core Modeling Product Management > >> Schrödinger, Inc. > >> > >> (e) jason.vertr...@schrodinger.com > >> (o) +1 (603) 374-7120 > > > > > > > > -- > Jason Vertrees, PhD > Director of Core Modeling Product Management > Schrödinger, Inc. > > (e) jason.vertr...@schrodinger.com > (o) +1 (603) 374-7120 > -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d___ 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] setting the cutoff radius that determines when atoms are bonded
Hi Rye, set connect_cutoff, 0.5 load 1.xyz produces different bonding than if you left the connect_cutoff value to its default, 0.35. Set it to 0.85 and then load the file and you'll see the Unknown atoms in the middle bonded as well. Cheers, -- Jason On Tue, Dec 4, 2012 at 11:33 AM, Rye Terrell wrote: > > Hi Jason, > > Thanks for the tip. I still couldn't get it to work. I'll google around some > more, but here's the file. Thanks for any help. > > Cheers, > Rye > > > On Mon, Dec 3, 2012 at 4:34 PM, Jason Vertrees > wrote: >> >> Hi Rye, >> >> How about connect_cutoff in Å? There's also connect_mode >> (http://www.pymolwiki.org/index.php/Connect_mode). >> >> If you send me a copy of your file I can look at it. >> >> Cheers, >> >> -- Jason >> >> On Mon, Dec 3, 2012 at 4:03 PM, Rye Terrell >> wrote: >> > I have a silicon bulk system. Pymol indicates that a handful of the >> > atoms >> > are bonded to each other. Many bonds are not indicated. Is there some >> > value >> > I can adjust that will make pymol indicate that more atoms are bonded? I >> > usually do this by setting some cutoff radius, but googling around has >> > yielded no results. I see that there is a way to bond atom pairs >> > manually, >> > but that would be incredibly tedious given the number of bonds there >> > should >> > be. >> > >> > Thanks for any help! >> > Rye >> > >> > >> > -- >> > Keep yourself connected to Go Parallel: >> > BUILD Helping you discover the best ways to construct your parallel >> > projects. >> > http://goparallel.sourceforge.net >> > ___ >> > 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 >> >> >> >> -- >> Jason Vertrees, PhD >> Director of Core Modeling Product Management >> Schrödinger, Inc. >> >> (e) jason.vertr...@schrodinger.com >> (o) +1 (603) 374-7120 > > -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ 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] setting the cutoff radius that determines when atoms are bonded
Hi Jason, Thanks for the tip. I still couldn't get it to work. I'll google around some more, but here's the file. Thanks for any help. Cheers, Rye On Mon, Dec 3, 2012 at 4:34 PM, Jason Vertrees < jason.vertr...@schrodinger.com> wrote: > Hi Rye, > > How about connect_cutoff in Å? There's also connect_mode > (http://www.pymolwiki.org/index.php/Connect_mode). > > If you send me a copy of your file I can look at it. > > Cheers, > > -- Jason > > On Mon, Dec 3, 2012 at 4:03 PM, Rye Terrell > wrote: > > I have a silicon bulk system. Pymol indicates that a handful of the atoms > > are bonded to each other. Many bonds are not indicated. Is there some > value > > I can adjust that will make pymol indicate that more atoms are bonded? I > > usually do this by setting some cutoff radius, but googling around has > > yielded no results. I see that there is a way to bond atom pairs > manually, > > but that would be incredibly tedious given the number of bonds there > should > > be. > > > > Thanks for any help! > > Rye > > > > > -- > > Keep yourself connected to Go Parallel: > > BUILD Helping you discover the best ways to construct your parallel > > projects. > > http://goparallel.sourceforge.net > > ___ > > 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 > > > > -- > Jason Vertrees, PhD > Director of Core Modeling Product Management > Schrödinger, Inc. > > (e) jason.vertr...@schrodinger.com > (o) +1 (603) 374-7120 > 1.xyz Description: Protein Databank data -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d___ 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
