VMD-L Mailing List

From: sollebac (sollebac_at_gmail.com)
Date: Fri Mar 29 2013 - 12:23:14 CDT

Hi John,

Thank you very much for your answer , i appreciate it
>I assume you are talking about the "Material" setting for a
graphical representation, yes?
Yes, exactly

>What does VMD print in your
>startup messages in the section about OpenGL?
When vmd starts up the output print is:

Info) VMD for LINUXAMD64, version 1.9.1 (March 28, 2013)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 2 CPUs detected.
Info) Free system memory: 2810MB (75%)
Warning) Detected X11 'Composite' extension: if incorrect display occurs
Warning) try disabling this optional X server feature.
Info) OpenGL renderer: Mesa DRI R600 (RS880 9712) 20090101 TCL DRI2
Info) Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVF)
Info) Full GLSL rendering mode is available.
Info) Textures: 2-D (4096x4096), 3-D (256x256x256), Multitexture (8)

it's all the output

>Does the issue with using the Transparent material change at all if
You switch on VMD Main|Display|Rendermode|GLSL?
Yea it works now, I changed to GLSL as you said, ( I haven't changed
before ..)
now i can make nice material representation transparent
thank you

Best regards
Jose Luis

On Fri, Mar 29, 2013 at 8:48 AM, John Stone <johns_at_ks.uiuc.edu> wrote:

> Hi,
> When you are referring to a "transparent" option in your email
> below, I assume you are talking about the "Material" setting for a
> graphical representation, yes? If changing the default material
> for a representation from "Opaque" to "Transparent" has no visible
> effect, then most likely you are encountering some sort of problem with
> the OpenGL graphics driver for your GPU. What does VMD print in your
> startup messages in the section about OpenGL? You should see something
> like this when VMD starts up, tell me what yours says:
>
> Info) OpenGL renderer: GeForce GTX 285/PCI/SSE2
> Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVFG)
> Info) Full GLSL rendering mode is available.
> Info) Textures: 2-D (8192x8192), 3-D (2048x2048x2048), Multitexture (4)
>
> Does the issue with using the Transparent material change at all if
> you switch on VMD Main|Display|Rendermode|GLSL?
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Mar 29, 2013 at 01:55:20AM -0600, sollebac wrote:
> > Dear vmd users,
> > I successfully installed vmd 1.9.1 in ubuntu 10. , there are not
> errors
> > when it star up ... seems that everything works fine !!
> > but when i try to plot, for example the electronic density (load from
> > cube file) the option "transparent" does not works, nothing happens!!
> > It could be a simple question but im not able to solve it and i hope
> you
> > can help me.
> > im doing something wrong or I need to install other plugins or
> scripts
> > in order to active this options? (transparent) , ( i want to make
> the
> > density(cube) transparent)
> > my options for compilation were:
> > ./configure LINUXAMD64 OPENGL FLTK TK IMD NETCDF TCL PYTHON PTHREADS
> > NUMPY SILENT
> > any advice is welcome
> > thanks in advance
> > Jose Luis
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>