pymol-users

[PyMOL] maximum sphere-quality ?

[Xiao-Ping Z. <xp...@uc...>]

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

Re: [PyMOL] maximum sphere-quality ?

[Jason V. <jas...@sc...>]

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

Re: [PyMOL] maximum sphere-quality ?

[Xiao-Ping Z. <xp...@uc...>]

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...
> >
> 
> 
> 

Re: [PyMOL] maximum sphere-quality ?

[Tsjerk W. <ts...@gm...>]

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

Re: [PyMOL] maximum sphere-quality ?

[Xiao-Ping Z. <xp...@uc...>]

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...