From: William S. <wg...@ch...> - 2007-05-21 17:00:38
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Is it possible to create a 3D pdf using pymol? William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/ |
From: nick h. <nic...@gm...> - 2007-05-21 18:41:16
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On 5/21/07, William Scott <wg...@ch...> wrote: > > Is it possible to create a 3D pdf using pymol? It most certainly is possible, albeit not directly. What type of stereo image are you trying to output? The ray functionality in pymol will output stereo pairs which are meant for either wall-eye or cross-eye display. The default output format is PNG, you can easily output a high-resolution png image and convert it to PDF format afterwards. Open Office will export to PDFs natively, and is free. Using the ghostscript package in linux, this conversion can be automated if you're looking for more than a one-off production. If you're trying to generate anaglyph images (red/blue glasses), it also is possible, but requires some scripting. Feel free to contact me for more details. -Nick |
From: Tsjerk W. <ts...@gm...> - 2007-05-21 20:41:31
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Hi William, In contrast to Nick, I read your question as inquiring after a 3D probability density function. In case I get it wrong, just ignore this mail. It is well possible to generate 3D pdfs and display them in Pymol. Actually, for one project I'm doing that right now. I have modified a program from the Gromacs package to generate xplor density maps of relative occupancies in space. Something similar may be of use to you. If you want, I can send you the program, or a script which does a similar thing. Alternatively, I can just send the routine to write an xplor map, given a 3D array (C code, though maybe I already have it in python too). Hope it helps, Tsjerk On 5/21/07, William Scott <wg...@ch...> wrote: > Is it possible to create a 3D pdf using pymol? > > > William G. Scott > > Contact info: > http://chemistry.ucsc.edu/~wgscott/ > > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 |
From: William S. <wg...@ch...> - 2007-05-21 21:09:17
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Sorry, I meant 3D pdf (Adoobie portable document format). But what you are doing sounds pretty cool. Please announce it when you are ready Tsjerk Wassenaar wrote: > Hi William, > > In contrast to Nick, I read your question as inquiring after a 3D > probability density function. In case I get it wrong, just ignore this > mail. > It is well possible to generate 3D pdfs and display them in Pymol. > Actually, for one project I'm doing that right now. I have modified a > program from the Gromacs package to generate xplor density maps of > relative occupancies in space. Something similar may be of use to you. > If you want, I can send you the program, or a script which does a > similar thing. Alternatively, I can just send the routine to write an > xplor map, given a 3D array (C code, though maybe I already have it in > python too). > > Hope it helps, > > Tsjerk > > On 5/21/07, William Scott <wg...@ch...> wrote: >> Is it possible to create a 3D pdf using pymol? >> >> >> William G. Scott >> >> Contact info: >> http://chemistry.ucsc.edu/~wgscott/ >> >> >> >> ------------------------------------------------------------------------- >> This SF.net email is sponsored by DB2 Express >> Download DB2 Express C - the FREE version of DB2 express and take >> control of your XML. No limits. Just data. Click to get it now. >> http://sourceforge.net/powerbar/db2/ >> _______________________________________________ >> PyMOL-users mailing list >> PyM...@li... >> https://lists.sourceforge.net/lists/listinfo/pymol-users >> > > > -- > Tsjerk A. Wassenaar, Ph.D. > Junior UD (post-doc) > Biomolecular NMR, Bijvoet Center > Utrecht University > Padualaan 8 > 3584 CH Utrecht > The Netherlands > P: +31-30-2539931 > F: +31-30-2537623 > |