Hi Troels,

yes I did try  many save name.idtf, selection / object / all / * 
and no output in the command window did appear...

thanks anyway,


Gianluigi



Da: Troels Emtekær Linnet <tlinnet@gmail.com>
A: Gianluigi Caltabiano <chimico01@yahoo.it>
Cc: "pymol-users@lists.sourceforge.net" <pymol-users@lists.sourceforge.net>
Inviato: Mercoledì 13 Marzo 2013 18:26
Oggetto: Re: [PyMOL] PyMOL to 3D PDF

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 line in the .tex file it exports.

Best
Troels

2013/3/13, Gianluigi Caltabiano <chimico01@yahoo.it>:
>
>
> 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 -62.45
> I did not have any line like this, not in the window panel neither in the
> idtf file. Where should I take this line?
>
> I used Hybrid PyMOL 1.5.0.3 on an iMAC.
>
> Thanks,
>
> Gianluigi
>
>
>
>
> ________________________________
>  Da: Troels Emtekær Linnet <tlinnet@gmail.com>
> A: Mike Marchywka <marchywka@hotmail.com>
> Cc: pymol-users@lists.sourceforge.net
> Inviato: Mercoledì 13 Marzo 2013 13:01
> Oggetto: Re: [PyMOL] PyMOL to 3D PDF
>
>
> 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 Marchywka <marchywka@hotmail.com>
>
>
>>
>>
>>----------------------------------------
>>> From: Blaine-Mooers@ouhsc.edu
>>> To: tlinnet@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.
>>> 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.
>>
>>
>>When you make 3D PDF how well do they display and manipulate? I thought
>> this would be a nice
>>feature for even 3D plots and IIRC tried it with an example from CRAN's R a
>> while back , I can't remember how it
>>came out in detail but seem to recall the pages took a while to load etc
>> and at the time it
>>was easier to load the data in an app rather than try to publish it that
>> way.  for many actual
>>pubs, they provide links in supplementary information section and it may be
>> just as easy to publish
>>a viewer script along with static images for illustration. A plugin would
>> be nice, I always liked CHIME
>>and that worked well on Internet Explorer about 10 years ago.
>>
>>
>>
>>>
>>>
>>>
>>> Blaine Mooers
>>> Assistant Professor
>>> Director Macromolecular Crystallography Lab
>>> Member Stephenson Cancer Center
>>> Department of Biochemistry and Molecular Biology
>>> University of Oklahoma Health Sciences Center
>>> S.L. Young Biomedical Research Center Rm. 466
>>>
>>> Letter address:
>>> P.O. Box 26901, BRC 466
>>> Oklahoma City, OK 73190
>>>
>>> Shipping address:
>>> 975 NE 10th Street, BRC 466
>>> Oklahoma City, OK 73104-5419
>>>
>>> office: (405) 271-8300 lab: (405) 271-8313 fax: (405) 271-3910
>>>
>>> e-mail: blaine-mooers@ouhsc.edu
>>>
>>> Faculty webpage:
>>> http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/faculty/blaine-mooers-ph-d-
>>> X-ray lab webpage:
>>> http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/department-facilities/macromolecular-crystallography-laboratory
>>> SAXS Links webpage:
>>> http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/small-angle-x-ray-scattering-links.html?sfvrsn=0
>>>
>>> ________________________________________
>>> From: Troels Emtekær Linnet [tlinnet@gmail.com]
>>> Sent: Wednesday, March 13, 2013 4:19 AM
>>> To: Mooers, Blaine H.M. (HSC)
>>> Cc: pymol-users@lists.sourceforge.net
>>> Subject: Re: [PyMOL] PyMOL to 3D PDF
>>>
>>> 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
>>> window.
>>> I can import small molecules through. Files->Get MOL-> And then CAS
>>> number or smiles.
>>> For proteins I scoop into
>>> rcsb.org<https://urldefense.proofpoint.com/v1/url?u=http://rcsb.org&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0A&m=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0A&s=13813dfb4e17158190791d134f870a433ff7cc614007ae72c21c5a5810c10091>,
>>> and find the protein in the Jmol online viewer. (Just changing to white
>>> back ground).
>>>
>>> Right click in Jmol window->Export file->Export IDTF 3D model.
>>>
>>> That saves a .idtf file, and a .tex file ready for LaTeX.
>>> Rename the .idtf file, so it only ends on .idtf and not:
>>> filename.xyz.idtf
>>>
>>> Simpy converting the .idtf to .u3d as instructed in,
>>> http://www.pymolwiki.org/index.php/3d_pdf<https://urldefense.proofpoint.com/v1/url?u=http://www.pymolwiki.org/index.php/3d_pdf&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0A&m=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0A&s=25a32bf64cd6f0227c7a8a73361f42721f9a6a377010deef4b50acdb49f29ccd>)
>>> and you are ready to go from the given .tex file. (Removing the last
>>> looong comment section.)
>>>
>>> With a little practice, it only takes 3 min, to have 3d implementation of
>>> your molecule
>>> in teaching material / beamer presentation.
>>>
>>> I wish that could be implemented in PyMOL, and I have been looking for a
>>> wish list,
>>> but I don't know where that exists?
>>>
>>> Best
>>>
>>> Troels Emtekær Linnet
>>> Ved kløvermarken 9,
>>> 1.th<https://urldefense.proofpoint.com/v1/url?u=http://1.th&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0A&m=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0A&s=5edb01bafbd605fcdadfe489b90dfe0d526e9a96b0ba86b04791e8d92bc46a63>
>>> 2300 København S
>>> Mobil: +45 60210234
>>>
>>>
>>> 2013/3/12 Mooers, Blaine H.M. (HSC)
>>> <Blaine-Mooers@ouhsc.edu<mailto:Blaine-Mooers@ouhsc.edu>>
>>> I saw Jason Vertrees update of
>>> http://www.pymolwiki.org/index.php/3d_pdf<https://urldefense.proofpoint.com/v1/url?u=http://www.pymolwiki.org/index.php/3d_pdf&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0A&m=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0A&s=25a32bf64cd6f0227c7a8a73361f42721f9a6a377010deef4b50acdb49f29ccd>.
>>> It has the address to the source code for u3d-1.4.3. I could not compile
>>> earlier
>>> versions of this program on a Mac running Snow Leopard, but I had
>>> success with this version. I followed Jason's directions for compiling on
>>> Linux through chmod g+wx. I had installed cmake earlier.
>>>
>>> The program compiles fine on Ubuntu 12.04 too.
>>>
>>> I used pdflatex from fink with beamer and the movies15 package.
>>>
>>>
>>> Blaine Mooers
>>> Assistant Professor
>>> Director Macromolecular Crystallography Lab
>>> Member Stephenson Cancer Center
>>> Department of Biochemistry and Molecular Biology
>>> University of Oklahoma Health Sciences Center
>>> S.L. Young Biomedical Research Center Rm. 466
>>>
>>> Letter address:
>>> P.O. Box 26901, BRC 466
>>> Oklahoma City, OK 73190
>>>
>>> Shipping address:
>>> 975 NE 10th Street, BRC 466
>>> Oklahoma City, OK 73104-5419
>>>
>>> office: (405) 271-8300 lab: (405) 271-8313 fax: (405) 271-3910
>>>
>>> e-mail: blaine-mooers@ouhsc.edu<mailto:blaine-mooers@ouhsc.edu>
>>>
>>> Faculty webpage:
>>> http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/faculty/blaine-mooers-ph-d-
>>> X-ray<https://urldefense.proofpoint.com/v1/url?u=http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/faculty/blaine-mooers-ph-d-%2520X-ray&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0A&m=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0A&s=7effd9a5dfc7406f62b612b40552c3ff1db33051b259ac785358f3b82708b6bb>
>>> lab webpage:
>>> http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/department-facilities/macromolecular-crystallography-laboratory<https://urldefense.proofpoint.com/v1/url?u=http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/department-facilities/macromolecular-crystallography-laboratory&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0A&m=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0A&s=974ecd1dbde88223553e3af3fa345386f53ff187ea5ed34118851de8b8412aa2>
>>> SAXS Links webpage:
>>> http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/small-angle-x-ray-scattering-links.html?sfvrsn=0<https://urldefense.proofpoint.com/v1/url?u=http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/small-angle-x-ray-scattering-links.html?sfvrsn%3D0&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0A&m=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0A&s=5d4e1e063b313cb193ae4e8a88770724f44a2c438c85e69e833c3d7f2afa9729>
>>>
>>> ------------------------------------------------------------------------------
>>> Everyone hates slow websites. So do we.
>>> Make your web apps faster with AppDynamics
>>> Download AppDynamics Lite for free today:
>>> http://p.sf.net/sfu/appdyn_d2d_mar<https://urldefense.proofpoint.com/v1/url?u=http://p.sf.net/sfu/appdyn_d2d_mar&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0A&m=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0A&s=e69f9a186785d4669c6f642dfd0cf9e233a0733becb22fce98f1b2216549c40c>
>>> _______________________________________________
>>> PyMOL-users mailing list
>>> (PyMOL-users@lists.sourceforge.net<mailto:PyMOL-users@lists.sourceforge.net>)
>>> Info Page:
>>> https://lists.sourceforge.net/lists/listinfo/pymol-users<https://urldefense.proofpoint.com/v1/url?u=https://lists.sourceforge.net/lists/listinfo/pymol-users&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0A&m=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0A&s=27578b0acd8417ee5ad041b8fb3405e11533086c77123f6c89d8eb5ab3687a96>
>>> Archives:
>>> http://www.mail-archive.com/pymol-users@lists.sourceforge.net<https://urldefense.proofpoint.com/v1/url?u=http://www.mail-archive.com/pymol-users%40lists.sourceforge.net&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0A&m=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0A&s=3361c0409e75f1296ae346ff46b307f7fcc1bc6a3274c663c132d87b299bf7a6>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Everyone hates slow websites. So do we.
>>> Make your web apps faster with AppDynamics
>>> Download AppDynamics Lite for free today:
>>> http://p.sf.net/sfu/appdyn_d2d_mar
>>
>>> _______________________________________________
>>> 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
>>
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_mar
> _______________________________________________
> 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


--

Troels Emtekær Linnet
Ved kløvermarken 9, 1.th
2300 København S
Mobil: +45 60210234