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[PyMOL] Re: PyMOL-users digest, Vol 1 #633 - 2 msgs
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From: Jason V. <tr...@ve...> - 2004-07-02 16:00:51
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Gabriel, I've managed to render scenes for a movie that had well over 100,000 atoms. For stills, I've rendered a nucleocapsid of over 292,000 atoms. So, I'm sure it can be done. I think the real large render only took a few minutes as well. -- Jason On Wed, 2004-06-30 at 22:47, pym...@li... wrote: > Send PyMOL-users mailing list submissions to > pym...@li... > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/pymol-users > or, via email, send a message with subject or body 'help' to > pym...@li... > > You can reach the person managing the list at > pym...@li... > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of PyMOL-users digest..." > > > Today's Topics: > > 1. large molecules (Gabriel C. Lander) > 2. Re: large molecules (Luca Jovine) > > --__--__-- > > Message: 1 > To: pym...@li... > From: "Gabriel C. Lander" <gl...@sc...> > Date: Wed, 30 Jun 2004 08:39:37 -0700 > Subject: [PyMOL] large molecules > > Anyone know if pymol can in any way handle rendering very large > molecules (like viral capsids)? I've got a molecule with 392,095 > atoms, and an additional 78,406 - atom molecule with 155 different > states. Pymol loads the line rendering just fine, but when I go to > cartoon rendering, Pymol crashes. I'm using 2 dual-processor G5's. > Is there any way to get this to work? > thanks, > -gabe > > > > --__--__-- > > Message: 2 > Cc: Mailing List PyMol Users <pym...@li...> > From: Luca Jovine <luc...@ma...> > Subject: Re: [PyMOL] large molecules > Date: Wed, 30 Jun 2004 12:09:43 -0400 > To: "Gabriel C. Lander" <gl...@sc...> > > > --Apple-Mail-2-782917697 > Content-Transfer-Encoding: 7bit > Content-Type: text/plain; > charset=US-ASCII; > format=flowed > > On Jun 30, 2004, at 11:39, Gabriel C. Lander wrote: > > > Anyone know if pymol can in any way handle rendering very large > > molecules (like viral capsids)? I've got a molecule with 392,095 > > atoms, and an additional 78,406 - atom molecule with 155 different > > states. Pymol loads the line rendering just fine, but when I go to > > cartoon rendering, Pymol crashes. I'm using 2 dual-processor G5's. > > Is there any way to get this to work? > > thanks, > > -gabe > > Hi Gabe, > > I don't know about viral capsids, but I could render the whole 50S > subunit (~90000 atoms) with no problems (see > http://www.mssm.edu/students/jovinl02/images/50s_large.jpg ) - that is, > after reducing the hash_max parameter to 70 (default is 120) to prevent > PyMOL from crashing. > Another two parameters you might want to reduce are stick_quality > (default is 8) and cartoon_sampling (default is 7); lowering these will > save a lot of memory and not highly affect the quality of an overall > view of something as large as a virus... I doubt people will check > individual strands within such a picture! > > Hope this helps, good luck - Luca > > -------------------------------------------------------- > Luca Jovine, Ph.D. > Brookdale Department of Molecular, Cell & Developmental Biology > Mount Sinai School of Medicine > Annenberg Building, Room 25-18 > One Gustave L. Levy Place, New York, NY 10029-6574, USA > Voice: +1.212.241-8620 FAX: +1.509.356-2832 > E-Mail: luc...@ma... - luc...@ms... > W3: http://www.mssm.edu/students/jovinl02 > -------------------------------------------------------- > > --Apple-Mail-2-782917697 > Content-Transfer-Encoding: 7bit > Content-Type: text/enriched; > charset=US-ASCII > > On Jun 30, 2004, at 11:39, Gabriel C. Lander wrote: > > > <excerpt>Anyone know if pymol can in any way handle rendering very > large molecules (like viral capsids)? I've got a molecule with > 392,095 atoms, and an additional 78,406 - atom molecule with 155 > different states. Pymol loads the line rendering just fine, but when > I go to cartoon rendering, Pymol crashes. I'm using 2 dual-processor > G5's. > > Is there any way to get this to work? > > thanks, > > -gabe > > </excerpt> > > Hi Gabe, > > > I don't know about viral capsids, but I could render the whole 50S > subunit (~90000 atoms) with no problems (see > http://www.mssm.edu/students/jovinl02/images/50s_large.jpg ) - that > is, after reducing the hash_max parameter to 70 (default is 120) to > prevent PyMOL from crashing. > > Another two parameters you might want to reduce are stick_quality > (default is 8) and cartoon_sampling (default is 7); lowering these > will save a lot of memory and not highly affect the quality of an > overall view of something as large as a virus... I doubt people will > check individual strands within such a picture! > > > Hope this helps, good luck - Luca > > > <fontfamily><param>Helvetica</param>-------------------------------------------------------- > > Luca Jovine, Ph.D. > > Brookdale Department of Molecular, Cell & Developmental Biology > > Mount Sinai School of Medicine > > Annenberg Building, Room 25-18 > > One Gustave L. Levy Place, New York, NY 10029-6574, USA > > Voice: +1.212.241-8620 FAX: +1.509.356-2832 > > E-Mail: luc...@ma... - luc...@ms... > > W3: http://www.mssm.edu/students/jovinl02 > > --------------------------------------------------------</fontfamily> > > > --Apple-Mail-2-782917697-- > > > > > --__--__-- > > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > End of PyMOL-users Digest |
