VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu Jul 23 2009 - 12:29:49 CDT

On Thu, 2009-07-23 at 13:21 -0400, Stanislav Polonsky wrote:
> (1) Thank you, Axel! I'd rather wait for interactive 1.8.7 on AIX.
>
> (2) FYI: I played a bit with 1.8.7 beta 5 on AIX: it relies to rlwrap
> command which is not present on default AIX distribution.

that has been fixed. the launch script will only
look for rlwrap on linux machines now.

cheers,
   axel.

>
> Stas Polonsky, PhD
> Research Staff Member
> IBM T.J. Watson Research Center
> (914) 945-3849
>
>
>
> Inactive hide details for Axel Kohlmeyer
> <akohlmey_at_cmm.chem.upenn.edu>Axel Kohlmeyer
> <akohlmey_at_cmm.chem.upenn.edu>
>
>
> Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu>
> Sent by: Axel Kohlmeyer <akohlmey_at_gmail.com>
>
> 07/23/2009 12:23 PM
>
>
> To
>
> Stanislav
> Polonsky/Watson/IBM_at_IBMUS
>
> cc
>
> John Stone
> <johns_at_ks.uiuc.edu>, vmd-l_at_ks.uiuc.edu
>
> Subject
>
> Re: vmd-l:
> Problem:
> volumetric data
> coloring fails on
> AIX5_64 with
> GXT6500 OpenGL
> renderer
>
>
>
> On Thu, 2009-07-23 at 11:39 -0400, Stanislav Polonsky wrote:
> > Hi Axel,
>
> stas,
>
> > I'm going to follow your advice and use VMD beta5 with
> InternalTachyon
> > renderer. When I look at VMD downloads directory I see "AIX6_64
> > Text-mode" for AIX. Before I proceed with installation I wonder what
> > does "Text-mode" mean and if this "Text-mode" might prevent me from
> > using volumetric data coloring?
>
> it means you won't have an interactive graphical display.
> this compile is meant to be used for batch execution of
> analysis scripts but might be able to do the rendering
> as well. i've never tried anything like this.
>
> what you get is the same as if you'd start VMD with
> vmd -dispdev text
> in your case that means, you have to prepare a script
> file, e.g. via "Save State..." elsewhere and then use
> "play saved_state.vmd" on the vmd command line.
>
> if you can wait a few more days, there should be a final
> release for VMD (john is working very hard to get it done),
> and i assume also a binary with interactive graphics support
> for AIX will show up.
>
> cheers,
> axel.
>
> >
> > Stas Polonsky, PhD
> > Research Staff Member
> > IBM T.J. Watson Research Center
> > (914) 945-3849
> >
> >
> >
> > Inactive hide details for Axel Kohlmeyer
> > <akohlmey_at_cmm.chem.upenn.edu>Axel Kohlmeyer
> > <akohlmey_at_cmm.chem.upenn.edu>
> >
> >
> > Axel Kohlmeyer
> <akohlmey_at_cmm.chem.upenn.edu>
> > Sent by: owner-vmd-l_at_ks.uiuc.edu
> >
> > 07/20/2009 04:43 PM
> >
> >
> > To
> >
> > Stanislav
> > Polonsky/Watson/IBM_at_IBMUS
> >
> > cc
> >
> > John Stone
> > <johns_at_ks.uiuc.edu>, vmd-l_at_ks.uiuc.edu
> >
> > Subject
> >
> > Re: vmd-l:
> > Problem:
> > volumetric data
> > coloring fails on
> > AIX5_64 with
> > GXT6500 OpenGL
> > renderer
> >
> >
> >
> > On Mon, 2009-07-20 at 14:16 -0400, Stanislav Polonsky wrote:
> > > Thank you guys for your fast help!
> >
> > as a somewhat cumbersome workaround, you could also try to use
> > the Render dialog and using the InternalTachyon renderer,
> > provided you have installed the latest VMD beta5 version.
> >
> > cheers,
> > axel.
> >
> > > Stas Polonsky, PhD
> > > Research Staff Member
> > > IBM T.J. Watson Research Center
> > > (914) 945-3849
> > >
> > >
> > >
> > > Inactive hide details for John Stone <johns_at_ks.uiuc.edu>John Stone
> > > <johns_at_ks.uiuc.edu>
> > >
> > >
> > > John Stone <johns_at_ks.uiuc.edu>
> > >
> > > 07/20/2009 12:43 PM
> > >
> > >
> > > To
> > >
> > > Stanislav
> > > Polonsky/Watson/IBM_at_IBMUS
> > >
> > > cc
> > >
> > > vmd-l_at_ks.uiuc.edu
> > >
> > > Subject
> > >
> > > Re: vmd-l:
> > > Problem:
> > > volumetric data
> > > coloring fails on
> > > AIX5_64 with
> > > GXT6500 OpenGL
> > > renderer
> > >
> > >
> > >
> > >
> > > Stas,
> > > Yes, your graphics card is unable to support 3-D texture mapping.
> > > You'll need a better card in order to display the potential maps
> on
> > > your
> > > system. Since you're running AIX, I assume this is an
> IBM-produced
> > > video
> > > card, and you probably can't simply use an NVIDIA card or
> something
> > > similar.
> > > If it were a linux PC, that would be the easiest option for an
> > > upgrade.
> > > I'd check with your local computer people and see what other video
> > > card/GPU
> > > options are available for your system, and either upgrade the
> video
> > > card, or
> > > consider running VMD on a different machine with a better GPU when
> > you
> > > want
> > > to view potential maps etc.
> > >
> > > Cheers,
> > > John Stone
> > > vmd_at_ks.uiuc.edu
> > >
> > > On Mon, Jul 20, 2009 at 12:40:40PM -0400, Stanislav Polonsky
> wrote:
> > > > Hi John,
> > > >
> > > > Thanks for the fast response. Below is the startup message. I
> > can
> > > see it
> > > > says 2-D textures :-(
> > > >
> > > > Info) Textures: 2-D (2048x2048), Multitexture (2)
> > > >
> > > > I guess my only option is getting a new graphics card?
> > > >
> > > > Stas Polonsky, PhD
> > > > Research Staff Member
> > > > IBM T.J. Watson Research Center
> > > > (914) 945-3849
> > > >
> > > > Inactive hide details for John Stone <johns_at_ks.uiuc.edu>John
> > > Stone
> > > > <johns_at_ks.uiuc.edu>
> > > >
> > > > John Stone To Stanislav
> > > Polonsky/Watson/IBM_at_IBMUS
> > > > <johns_at_ks.uiuc.edu> cc vmd-l_at_ks.uiuc.edu
> > >
> > > > Subject Re: vmd-l: Problem:
> > > volumetric data
> > > > 07/20/2009 12:29 PM coloring fails on
> > AIX5_64
> > > with
> > > > GXT6500 OpenGL
> renderer
> > >
> > > >
> > >
> > > >
> > > > Hi,
> > > > Can you send me your VMD text console startup messages?
> They
> > > should
> > > > indicate whether or not your video card/GPU is capable of
> > > supporting
> > > > 3-D texture mapping or not. If not, that would be the reason
> > > you're
> > > > not seeing the potential coloring...
> > > >
> > > > Cheers,
> > > > John Stone
> > > > vmd_at_ks.uiuc.edu
> > > >
> > > > On Mon, Jul 20, 2009 at 12:04:25PM -0400, Stanislav Polonsky
> > > wrote:
> > > > > Hi,
> > > > >
> > > > > When I load electrostatic potential data and select
> > > > > Graphics->Representations...->Draw Style tab->Coloring
> > > Method to
> > > > Volume
> > > > > all atoms become white. Selecting Trajectory tab and
> > playing
> > > with
> > > > Color
> > > > > Scale Data Range does not help. Please help!
> > > > >
> > > > > Stas Polonsky, PhD
> > > > > Research Staff Member
> > > > > IBM T.J. Watson Research Center
> > > > > (914) 945-3849
> > > >
> > > > --
> > > > NIH Resource for Macromolecular Modeling and Bioinformatics
> > > > Beckman Institute for Advanced Science and Technology
> > > > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > > > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > > > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> > >
> > >
> > >
> > >
> > >
> > > --
> > > NIH Resource for Macromolecular Modeling and Bioinformatics
> > > Beckman Institute for Advanced Science and Technology
> > > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> > >
> > >
> > >
> >
> > --
> >
> =======================================================================
> > Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu
> > http://www.cmm.upenn.edu
> > Center for Molecular Modeling -- University of Pennsylvania
> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA
> > 19104-6323
> > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel:
> 1-215-898-5425
> >
> =======================================================================
> > If you make something idiot-proof, the universe creates a better
> > idiot.
> >
> >
> >
> >
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu
> http://www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA
> 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better
> idiot.
>
>
>
> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.