Re: [PyMOL] PyMOL to 3D PDF

2013-03-13 Thread Troels Emtekær Linnet
Hi Gianluigi. The line goes into LaTeX. I guess it tells something about the center of the molecule, or some light settings. Have you tried: save pymol.idtf, all (or some other selection) The line should come out in the command window, like the get_view command. Jmol automatically write this li

Re: [PyMOL] PyMOL to 3D PDF

2013-03-13 Thread Gianluigi Caltabiano
Very interesting features! I have never tried and was trying to do it, following the tutorial in pymolwiki but at : * Save your molecule to an IDTF file in PyMOL: save pymol.idtf, * PyMOL will print a line that looks like: 3Daac=20.0, 3Droll=0, 3Dc2c=0 0 1, 3Droo=62.45, 3Dcoo=0 0 -62.4

Re: [PyMOL] PyMOL to 3D PDF

2013-03-13 Thread Mike Marchywka
I hit this link, the image was blank in evince but did come up in Adobe Reader 9 if I click on it ( also prompted for security issues) http://www.fys.ku.dk/~tlinnet/1zqa.pdf It was a bit sluggish but did  zoom and rotate acceptably. I guess in this  case the more useful thing would be all the i

Re: [PyMOL] PyMOL to 3D PDF

2013-03-13 Thread Troels Emtekær Linnet
Hi Mike. Try the example pdfs at: http://pymolwiki.org/index.php/3d_pdf 1zqa PDF beamer 1zqa PDF Troels Emtekær Linnet Ved kløvermarken 9, 1.th 2300 København S Mobil: +45 60210234 2013/3/13 Mike Marchywk

Re: [PyMOL] PyMOL to 3D PDF

2013-03-13 Thread Mike Marchywka
> From: blaine-moo...@ouhsc.edu > To: tlin...@gmail.com > Date: Wed, 13 Mar 2013 04:45:59 -0500 > CC: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] PyMOL to 3D PDF > > PyMOL will also save surfaces in addition to cartoons to vwrl and idtf. > An

Re: [PyMOL] PyMOL to 3D PDF

2013-03-13 Thread Mooers, Blaine H.M. (HSC)
PyMOL will also save surfaces in addition to cartoons to vwrl and idtf. Any representation composed of triangular surfaces should work. Thus, PuMOL fails to save labels to vmrl or idtf. This is another major advantage of JMOL over PyMOL at present. Blaine Mooers Assistant Professor Director

Re: [PyMOL] PyMOL to 3D PDF

2013-03-13 Thread Troels Emtekær Linnet
Yeah. That is a cool feature, and is kind of the "future" of publishing. :-) Or at least, a very powerful tool for teaching. *But it is sad that it only have cartoon export.* I wish that it could include other representations. For now I use Jmol, which can export the *whole representation in the