[PyMOL] Using Shaders

[QT]

Dear all,

Is there a way to use the shaders without the unsightly gaps in the models?

Shaders 
on
Shaders 
off

Best,
Quyen
--
Virtualization & Cloud Management Using Capacity Planning
Cloud computing makes use of virtualization - but cloud computing 
also focuses on allowing computing to be delivered as a service.
http://www.accelacomm.com/jaw/sfnl/114/51521223/___
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

Re: [PyMOL] Using Shaders

[Jason Vertrees]

Hi Quyen,

What kind of video card are you using? Based on the rendering I'm
guessing Quadro or Intel Mobile.

If Quadro try,

set cylinder_shader_ff_workaround, on

There is a known bug in some Quadro cards which this setting fixes.

Cheers,

-- Jason

On Wed, Feb 22, 2012 at 1:03 PM, QT  wrote:
> Dear all,
>
> Is there a way to use the shaders without the unsightly gaps in the models?
>
> Shaders on
> Shaders off
>
> Best,
> Quyen
>
>
> --
> Virtualization & Cloud Management Using Capacity Planning
> Cloud computing makes use of virtualization - but cloud computing
> also focuses on allowing computing to be delivered as a service.
> http://www.accelacomm.com/jaw/sfnl/114/51521223/
> ___
> 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



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrödinger, LLC

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

--
Virtualization & Cloud Management Using Capacity Planning
Cloud computing makes use of virtualization - but cloud computing 
also focuses on allowing computing to be delivered as a service.
http://www.accelacomm.com/jaw/sfnl/114/51521223/
___
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

[PyMOL] Error: Unreasonable connectivity in heteroatom, unsuccessful in guessing valences

[Rituparna Sengupta]

Hi,

I'm trying to make a plugin which calculates contact surface area for a set of 
ligands with a set of targets. I'm iterating the area calculation program 
through the list of ligands and targets to get the contact areas for the 
complex. I get the output fine but I keep getting an error. Does anyone know 
what it means?


 ObjectMoleculeGuessValences(1,0): Unreasonable connectivity in heteroatom,
  unsuccessful in guessing valences.



Thanks,
Ritu

--
Virtualization & Cloud Management Using Capacity Planning
Cloud computing makes use of virtualization - but cloud computing 
also focuses on allowing computing to be delivered as a service.
http://www.accelacomm.com/jaw/sfnl/114/51521223/
___
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

Re: [PyMOL] Using Shaders

[QT]

Dear Jason,

I have two GeForce GTS 450.  They're not sli.  The driver is pretty new.

The gap glitch has miraculously gone away...I do not know why.  Also I
didn't mention that the rendering from from a 1.3 session file, but I don't
think that matters?

The "set cylinder_shader_ff_workaround, on" does put things in the right
perspective though.

cylinder_shader_ff_workaround,
off
cylinder_shader_ff_workaround,
on

Best,
Quyen

Below is a snippet of the glxinfo.


[quyen@ribo Crystals]$ vglrun glxinfo
name of display: :1.0
display: :1  screen: 0
direct rendering: Yes
server glx vendor string: VirtualGL
server glx version string: 1.4
server glx extensions:
GLX_ARB_get_proc_address, GLX_ARB_multisample, GLX_EXT_visual_info,
GLX_EXT_visual_rating, GLX_SGI_make_current_read, GLX_SGIX_fbconfig,
GLX_SGIX_pbuffer, GLX_SUN_get_transparent_index, GLX_ARB_create_context
client glx vendor string: VirtualGL
client glx version string: 1.4
client glx extensions:
GLX_ARB_get_proc_address, GLX_ARB_multisample, GLX_EXT_visual_info,
GLX_EXT_visual_rating, GLX_SGI_make_current_read, GLX_SGIX_fbconfig,
GLX_SGIX_pbuffer, GLX_SUN_get_transparent_index, GLX_ARB_create_context
GLX version: 1.4
GLX extensions:
GLX_ARB_get_proc_address, GLX_ARB_multisample, GLX_EXT_visual_info,
GLX_EXT_visual_rating, GLX_SGI_make_current_read, GLX_SGIX_fbconfig,
GLX_SGIX_pbuffer, GLX_SUN_get_transparent_index, GLX_ARB_create_context
OpenGL vendor string: NVIDIA Corporation
OpenGL renderer string: GeForce GTS 450/PCI/SSE2
OpenGL version string: 4.1.0 NVIDIA 280.13
OpenGL shading language version string: 4.10 NVIDIA via Cg compiler
=

On Wed, Feb 22, 2012 at 12:30 PM, Jason Vertrees <
jason.vertr...@schrodinger.com> wrote:

> Hi Quyen,
>
> What kind of video card are you using? Based on the rendering I'm
> guessing Quadro or Intel Mobile.
>
> If Quadro try,
>
> set cylinder_shader_ff_workaround, on
>
> There is a known bug in some Quadro cards which this setting fixes.
>
> Cheers,
>
> -- Jason
>
> On Wed, Feb 22, 2012 at 1:03 PM, QT  wrote:
> > Dear all,
> >
> > Is there a way to use the shaders without the unsightly gaps in the
> models?
> >
> > Shaders on
> > Shaders off
> >
> > Best,
> > Quyen
> >
> >
> >
> --
> > Virtualization & Cloud Management Using Capacity Planning
> > Cloud computing makes use of virtualization - but cloud computing
> > also focuses on allowing computing to be delivered as a service.
> > http://www.accelacomm.com/jaw/sfnl/114/51521223/
> > ___
> > 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
>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrödinger, LLC
>
> (e) jason.vertr...@schrodinger.com
> (o) +1 (603) 374-7120
>
--
Virtualization & Cloud Management Using Capacity Planning
Cloud computing makes use of virtualization - but cloud computing 
also focuses on allowing computing to be delivered as a service.
http://www.accelacomm.com/jaw/sfnl/114/51521223/___
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

Re: [PyMOL] Error: Unreasonable connectivity in heteroatom, unsuccessful in guessing valences

[Jason Vertrees]

Hi Rituparna,

Older version of PyMOL output this when confused regarding the
hetereoatom/ligand structure. Do you have proper chemistry? Does the
ligand look correct when shown on screen?

Cheers,

-- Jason

On Wed, Feb 22, 2012 at 5:02 PM, Rituparna Sengupta  wrote:
> Hi,
>
> I'm trying to make a plugin which calculates contact surface area for a set 
> of ligands with a set of targets. I'm iterating the area calculation program 
> through the list of ligands and targets to get the contact areas for the 
> complex. I get the output fine but I keep getting an error. Does anyone know 
> what it means?
>
>
>  ObjectMoleculeGuessValences(1,0): Unreasonable connectivity in heteroatom,
>   unsuccessful in guessing valences.
>
>
>
> Thanks,
> Ritu
>
> --
> Virtualization & Cloud Management Using Capacity Planning
> Cloud computing makes use of virtualization - but cloud computing
> also focuses on allowing computing to be delivered as a service.
> http://www.accelacomm.com/jaw/sfnl/114/51521223/
> ___
> 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



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrödinger, LLC

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

--
Virtualization & Cloud Management Using Capacity Planning
Cloud computing makes use of virtualization - but cloud computing 
also focuses on allowing computing to be delivered as a service.
http://www.accelacomm.com/jaw/sfnl/114/51521223/
___
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