From: Xiao-Ping Z. <xp...@uc...> - 2010-10-27 21:09:30
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Hi, PyMol users, I have noticed that Justin Lorieau (http:www.lorieau.commethods-and-referencemolecular-viewers30-pymol--ball-and-stick-figures.html) can use "set sphere_quality, 10" to generate a ball_stick picture. When I tried to use the same command, PyMol crashed. The default sphere_quality is 1, 3 is the maximum value that I can use. I am curious what is the maximum value. I am running PyMol 1.3 on Fedora 13. Thank you for your help. Xiao-Ping |
From: Jason V. <jas...@sc...> - 2010-10-27 21:28:18
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Hi Xiao-Ping, If you want the _best_ sphere quality, then try, set sphere_mode, 5 This is pixel-perfect rendering of spheres in PyMOL using openGL shaders. Otherwise, these quality settings in PyMOL are typically limited to how much memory your machine has; also, these settings are usually quadratic or exponential in their use of memory. That tutorial looks good, but needs updating to make better use of PyMOL's features. Cheers, -- Jason On Wed, Oct 27, 2010 at 5:09 PM, Xiao-Ping Zhang <xp...@uc...> wrote: > Hi, PyMol users, > > I have noticed that Justin Lorieau > (http://www.lorieau.com/methods-and-reference/molecular-viewers/30-pymol--ball-and-stick-figures.html) can use +ACI-set sphere+AF8-quality, 10+ACI to generate a ball+AF8-stick picture. When I tried to use the same command, PyMol crashed. The default sphere+AF8-quality is 1, 3 is the maximum value that I can use. I am curious what is the maximum value. I am running PyMol 1.3 on Fedora 13. > Thank you for your help. > > Xiao-Ping > > > > > ------------------------------------------------------------------------------ > Nokia and AT&T present the 2010 Calling All Innovators-North America contest > Create new apps & games for the Nokia N8 for consumers in U.S. and Canada > $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing > Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store > http://p.sf.net/sfu/nokia-dev2dev > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: Xiao-Ping Z. <xp...@uc...> - 2010-10-28 00:33:18
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Dear Jason, Thank you for your reply. I tried sphere_mode command on two machines. On Fedora 13, PyMol 1.3 set sphere_mode, 5 disabled sphere display. set sphere_mode, 4, 3, or 2 can show sphere, but it looks terrible. One Fedora 8, PyMol 1.3 set sphere_mode, 5 also disabled sphere display. But 4 gives a beautiful sphere view. It seems that I need to fix OpenGL on Fedora 13. Best regards, Xiao-Ping On Wed, 2010-10-27 at 17:27 -0400, Jason Vertrees wrote: > Hi Xiao-Ping, > > If you want the _best_ sphere quality, then try, > > set sphere_mode, 5 > > This is pixel-perfect rendering of spheres in PyMOL using openGL > shaders. Otherwise, these quality settings in PyMOL are typically > limited to how much memory your machine has; also, these settings are > usually quadratic or exponential in their use of memory. > > That tutorial looks good, but needs updating to make better use of > PyMOL's features. > > Cheers, > > -- Jason > > On Wed, Oct 27, 2010 at 5:09 PM, Xiao-Ping Zhang <xp...@uc...> wrote: > > Hi, PyMol users, > > > > I have noticed that Justin Lorieau > > (http:www.lorieau.commethods-and-referencemolecular-viewers30-pymol--ball-and-stick-figures.html) can use +ACI-set sphere+AF8-quality, 10+ACI to generate a ball+AF8-stick picture. When I tried to use the same command, PyMol crashed. The default sphere+AF8-quality is 1, 3 is the maximum value that I can use. I am curious what is the maximum value. I am running PyMol 1.3 on Fedora 13. > > Thank you for your help. > > > > Xiao-Ping > > > > > > > > > > ------------------------------------------------------------------------------ > > Nokia and AT&T present the 2010 Calling All Innovators-North America contest > > Create new apps & games for the Nokia N8 for consumers in U.S. and Canada > > $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing > > Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store > > http:p.sf.netsfunokia-dev2dev > > _______________________________________________ > > PyMOL-users mailing list (PyM...@li...) > > Info Page: https:lists.sourceforge.netlistslistinfopymol-users > > Archives: http:www...@li... > > > > > |
From: Tsjerk W. <ts...@gm...> - 2010-10-28 10:10:20
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Hi, The tutorial states that the quality needs to be increased prior to ray-tracing. But it seems to me that the {sphere,stick}_quality settings apply to the OpenGL rendering, whereas the raytracer uses 'real' spheres and cylinders. Even when setting sphere_quality to 0, 'ray' will still give (near) perfect spheres. Cheers, Tsjerk On Wed, Oct 27, 2010 at 11:27 PM, Jason Vertrees <jas...@sc...> wrote: > Hi Xiao-Ping, > > If you want the _best_ sphere quality, then try, > > set sphere_mode, 5 > > This is pixel-perfect rendering of spheres in PyMOL using openGL > shaders. Otherwise, these quality settings in PyMOL are typically > limited to how much memory your machine has; also, these settings are > usually quadratic or exponential in their use of memory. > > That tutorial looks good, but needs updating to make better use of > PyMOL's features. > > Cheers, > > -- Jason > > On Wed, Oct 27, 2010 at 5:09 PM, Xiao-Ping Zhang <xp...@uc...> wrote: >> Hi, PyMol users, >> >> I have noticed that Justin Lorieau >> (http://www.lorieau.com/methods-and-reference/molecular-viewers/30-pymol--ball-and-stick-figures.html) can use +ACI-set sphere+AF8-quality, 10+ACI to generate a ball+AF8-stick picture. When I tried to use the same command, PyMol crashed. The default sphere+AF8-quality is 1, 3 is the maximum value that I can use. I am curious what is the maximum value. I am running PyMol 1.3 on Fedora 13. >> Thank you for your help. >> >> Xiao-Ping >> >> >> >> >> ------------------------------------------------------------------------------ >> Nokia and AT&T present the 2010 Calling All Innovators-North America contest >> Create new apps & games for the Nokia N8 for consumers in U.S. and Canada >> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing >> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store >> http://p.sf.net/sfu/nokia-dev2dev >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... >> > > > > -- > Jason Vertrees, PhD > PyMOL Product Manager > Schrodinger, LLC > > (e) Jas...@sc... > (o) +1 (603) 374-7120 > > ------------------------------------------------------------------------------ > Nokia and AT&T present the 2010 Calling All Innovators-North America contest > Create new apps & games for the Nokia N8 for consumers in U.S. and Canada > $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing > Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store > http://p.sf.net/sfu/nokia-dev2dev > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands |
From: Xiao-Ping Z. <xp...@uc...> - 2010-10-28 00:04:08
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Dear Roger Rowlett, Thank you for your reply. I did run "set stick_ball, on" before "set sphere_quality, xx". Sincerely, Xiao-Ping On Wed, 2010-10-27 at 17:20 -0400, Roger Rowlett wrote: > See http:www.pymolwiki.orgindex.phpSphere_quality. > > On 10272010 5:09 PM, Xiao-Ping Zhang wrote: > > Hi, PyMol users, > > > > I have noticed that Justin Lorieau > > (http:www.lorieau.commethods-and-referencemolecular-viewers30-pymol--ball-and-stick-figures.html) can use "set sphere_quality, 10" to generate a ball_stick picture. When I tried to use the same command, PyMol crashed. The default sphere_quality is 1, 3 is the maximum value that I can use. I am curious what is the maximum value. I am running PyMol 1.3 on Fedora 13. > > Thank you for your help. > > > > Xiao-Ping > > > > > > > > > > ------------------------------------------------------------------------------ > > Nokia and AT&T present the 2010 Calling All Innovators-North America contest > > Create new apps & games for the Nokia N8 for consumers in U.S. and Canada > > $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing > > Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store > > http:p.sf.netsfunokia-dev2dev > > > > _______________________________________________ > > PyMOL-users mailing list (PyM...@li...) > > Info Page: https:lists.sourceforge.netlistslistinfopymol-users > > Archives: http:www...@li... |