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Re: [PyMOL] The Wiki appears outdated or in error
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From: James K. <jim...@kr...> - 2016-03-24 17:05:31
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Hi Jared, When I set geometry_export_mode, 1 in PyMOL, then save myfile.dae, then import into MeshLab, MeshLab hangs. Is there an alternative to MeshLab I can use to generate the u3d file? 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: <" rel="nofollow">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 23, 2016 10:53 PM To: jim...@kr... Cc: pymol-users <pym...@li...> Subject: Re: [PyMOL] The Wiki appears outdated or in error Hi Jim - This is something we've been talking about changing. The entire scene as viewed within PyMOL is inside that block, including the camera position. (The interior surface of the block itself provides the background color of the scene.) Some viewers, e.g. Mac Preview.app, default to displaying from the camera position, but others, including MeshLab, don't, which is understandably confusing. To export only the geometry without any of the scene information, you can `set geometry_export_mode, 1` in PyMOL before saving the .dae. Hope that helps! Cheers, Jared P.S. if you are able to work out a protocol/workflow for generating 3D PDFs that is better than what's on the wiki, I hope you will consider updating the wiki to help others who might try it in the future. Jared Sampson Columbia University On Mar 23, 2016, at 8:26 PM, James Kress <jim...@kr... <mailto:jim...@kr...> > wrote: I installed v 1.8.0.6 When I save ‘myfile.dae’ and then import into MeshLab, all I get is a solid gray block. What do I need to do in PyMOL to export my DNA structure? 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: <" rel="nofollow">http://www.kressworks.org/> http://www.kressworks.org Facebook: <" rel="nofollow">https://www.facebook.com/KressWorks.Foundation/> 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: Tuesday, March 22, 2016 1:40 PM To: jim...@kr... <mailto:jim...@kr...> Cc: pymol-users <pym...@li... <mailto:pym...@li...> > Subject: Re: [PyMOL] The Wiki appears outdated or in error Hi Jim - The COLLADA exporting code was incorporated into Open Source PyMOL starting with 1.7.3.2 (SVN 4097), but I'm not sure when it made it into Incentive PyMOL, so if that's what you're using, 1.7.4 might be just barely too early to have that capability. You could try saving as VRML2, (`save myfile.wrl`) and use MeshLab to convert that instead of the COLLADA file--I think VRML output is more complete than IDTF. Alternatively, you could install a more recent open source PyMOL using instructions available on the wiki: <" rel="nofollow">http://www.pymolwiki.org/index.php/Category:Installation> http://www.pymolwiki.org/index.php/Category:Installation. Cheers, Jared -- Jared Sampson Columbia University On Mar 21, 2016, at 5:46 PM, James Kress < <mailto:jim...@kr...> jim...@kr...> wrote: Hi Jared, The version of PyMOL I am using (1.7.4.0) does not recognize the dae file type. Here is the message PyMOL generates: PyMOL>save output_no_H2O.dae Save-Warning: Unrecognized file type -- defaulting to PDB format. Save: wrote "output_no_H2O.dae". I get the same error message if I use the command ‘save output_no_H2O.dae’ 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: <" rel="nofollow">http://www.kressworks.org/> http://www.kressworks.org Facebook: <" rel="nofollow">https://www.facebook.com/KressWorks.Foundation/> 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...> mailto:jm...@cu...] Sent: Wednesday, March 16, 2016 2:28 PM To: <mailto:jim...@kr...> jim...@kr... Cc: <mailto:pym...@li...> 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 < <mailto:jim...@kr...> 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 <" rel="nofollow">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: <" rel="nofollow">http://www.kressworks.org/> http://www.kressworks.org Facebook: <" rel="nofollow">https://www.facebook.com/KressWorks.Foundation/> 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. 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