Re: [Apbs-users] problem in displaying elec pot in surface

[Rute F. <fo...@bi...>]

 Hi,

 > there's no known solution other than to get a bug-free card.  If you tel=
l
 > me more about your system I should be able to give you more specific
 > suggestions.

I'm working on a machine (using Windows Vista) with these characteristics:

 Intel(R) Core 2 Duo T7250 (2.0GHz; 2MB Cache; FSB800)
 2GB SODIMM DDR2 667MHz exp a 4GB
 Intel 965GM
 Intel GMA X3100 at=E9 358MB partilhada

 What is your suggestion?

 Thanks a lot. :)

 Best,

 Rute

....................................
.Rute A R da Fonseca
.
.Genomics Group
.Department of Biology
.University of Copenhagen
.Universitetsparken 15, Building 10
.DK-2100 Copenhagen =D8
.Denmark
.
.Tel  : +45 35 32 12 12
.Email:fo...@bi...
....................................

> On 10/24/07, John Stone <jo...@ks...> wrote:
> >
> > Hi,
> >   Yes, black dots, geometric patterns, or other strange or unexpected
> > colorings typically indicate a broken graphics driver.  Depending on wh=
at
> > graphics card/driver you're using, you may be able to upgrade to a newe=
r
> > driver and the problem will go away.  For some other graphics chipsets/=
cards,
> >
> > Cheers,
> >   John Stone
> >   vm...@ks...
> >
> >
> >
> > On Wed, Oct 24, 2007 at 02:09:37PM -0500, Nathan Baker wrote:
> > > Hello --
> > >
> > > > I am trying to map the electrostatic potential onto a biomolecular
> > > > surface using VMD 1.8.6 and APBS 0.5.1. Somehow what I get is not a
> > > > surface totally coloured with the potential, but a black surface wi=
th
> > > > small geometric figures bearing the potential colours (see attached
> > > > picture).
> > >
> > > I have also seen this using VMD in conjunction with some graphics
> > > cards.  I'm Cc'ing John Stone, a VMD developer for more
> > > information/advice.
> > >
> > > > I followed all the steps of the tutorial (using the plugin with APB=
S)
> > > > and also tried creating the pot.dx file in standalone APBS and then
> > > > loading it into the pqr in VMD (since within VMD I was getting an
> > > > error message about a gamma keyword and thought it could be related=
).
> > > >
> > > > Can anyone give me some hint on what=B4s happening?
> > >
> > > I don't think this is user error; it is likely a problem with the
> > > graphics drivers.
> > >
> > > Sorry for the problems,
> > >
> > > Nathan
> > >
> > > > Thanks a lot!
> > > >
> > > > Best
> > > >
> > > > Rute
> > > >
> > > >
> > > > ....................................
> > > > .Rute A R da Fonseca               .
> > > > .                                  .
> > > > .Genomics Group                    .
> > > > .Department of Biology             .
> > > > .University of Copenhagen          .
> > > > .Universitetsparken 15, Building 10.
> > > > .DK-2100 Copenhagen =D8              .
> > > > .Denmark                           .
> > > > .                                  .
> > > > .Tel  : +45 35 32 12 12            .
> > > > .Email:fo...@bi...          .
> > > > ....................................
> > > >
> > > > ....................................
> > > > .Rute A R da Fonseca               .
> > > > .                                  .
> > > > .Genomics Group                    .
> > > > .Department of Biology             .
> > > > .University of Copenhagen          .
> > > > .Universitetsparken 15, Building 10.
> > > > .DK-2100 Copenhagen =D8              .
> > > > .Denmark                           .
> > > > .                                  .
> > > > .Tel  : +45 35 32 12 12            .
> > > > .Email:fo...@bi...          .
> > > > ....................................
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> > > >
> > > >
> > >
> > >
> > > --
> > > Associate Professor, Dept. of Biochemistry and Molecular Biophysics
> > > Center for Computational Biology, Washington University in St. Louis
> > > Web: http://cholla.wustl.edu/
> >
> > --
> > 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: jo...@ks...                 Phone: 217-244-3349
> >   WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078
> >
>