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Re: [PyMOL] The Wiki appears outdated or in error
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From: James K. <jim...@kr...> - 2016-03-16 18:31:59
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HI Jared, Thank you for your response. I will give it a try! Jim James Kress Ph.D., President The KressWorks® Foundation An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization “Engineering The Cure” © (248) 605-8770 Learn More and Donate At: Website: <http://www.kressworks.org/> http://www.kressworks.org Facebook: https://www.facebook.com/KressWorks.Foundation/ Twitter: @KressWorksFnd Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message. From: Sampson, Jared M. [mailto:jm...@cu...] Sent: Wednesday, March 16, 2016 2:28 PM To: jim...@kr... Cc: pym...@li... Subject: Re: [PyMOL] The Wiki appears outdated or in error Hi James - If I remember correctly, PyMOL's IDTF output currently only supports triangles meshes (not cylinders or spheres, e.g.), so unfortunately you're basically limited to surface representations for output directly into that format. As a workaround, you could try saving your scene in COLLADA format (`save myfile.dae`), and use an external program (e.g. Blender, Meshlab) to convert to IDTF or U3D. When doing so, please note that you'll probably need to `set collada_geometry_mode=1` to specifically use the subset of COLLADA elements supported by those two programs (they only allow <polylist> elements to describe the triangles, which are a more general, verbose description than the more concise <triangles> and <tristrips> output generated with the default setting). Hope that helps. Cheers, Jared -- Jared Sampson Columbia University On Mar 12, 2016, at 11:24 PM, James Kress <jim...@kr... <mailto:jim...@kr...> > wrote: Among the export functions, a particular interest of mine is the as a idtf file as "precursor" for a 3d pdf mentioned at <http://www.pymolwiki.org/index.php/3d_pdf> http://www.pymolwiki.org/index.php/3d_pdf where I experience difficulties I want to address here. While the export via the CLI works fine for creating a *.png picture or a VRML *.wrl-geometry, the similar export as *.idtf creates only a header to describe the scenery, but not the (expected) spheres and tubes to represent atoms and molecular bonds. The file generated is the same, regardless if I request the data export via save /home/user directory/target directory/test.idtf or the recommended save /home/user directory/target directory/test.idtf,* Marking/highlighting the molecule in question does not alter the situation. The relative orientation of the model in regard to the observer is provided, however, in the programs command line, like 3Daac=20.0, 3Droll=0, 3Dc2c=0 0 1, 3Droo=50.00, 3Dcoo=0 0 -50.00 In addition, there is no *.tex file written -- well in contrast to the pymol-wiki page -- that I would expect to be created in the very same directory, too. (This is contrast to jmol offering export as *.idtf while simultaneously writing a *.tex file, too.) Should I look up in a different directory instead? May be a mistake during the installation be a reason why I do not obtain (yet) a functional *.idtf? Do I need to load another / an additional plugin to enlarge the export functions? Thanks. Jim James Kress Ph.D., President The KressWorks® Foundation An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization “Engineering The Cure” © (248) 605-8770 Learn More and Donate At: Website: <http://www.kressworks.org/> http://www.kressworks.org Facebook: https://www.facebook.com/KressWorks.Foundation/ Twitter: @KressWorksFnd Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message. ------------------------------------------------------------------------------ Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. <http://pubads.g.doubleclick.net/gampad/clk?id=278785111&iu=/4140_______________________________________________> http://pubads.g.doubleclick.net/gampad/clk?id=278785111&iu=/4140_______________________________________________ PyMOL-users mailing list ( <mailto:PyM...@li...> PyM...@li...) Info Page: <https://lists.sourceforge.net/lists/listinfo/pymol-users> https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: <http://www.mail-archive.com/pym...@li...> http://www.mail-archive.com/pym...@li... |
