VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Mar 13 2007 - 10:21:19 CDT

Pawel,
  Great, I was hoping that'd solve your problem. You can draw a
color scale bar using the Visualization->Color Scale Bar plugin:
  http://www.ks.uiuc.edu/Research/vmd/plugins/colorscalebar/

The colors used by the color scale bar are those in the active
color scale. You can change the active color scale scheme in
the Graphics->Colors menu, in the Color Scale tab.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Mar 13, 2007 at 02:07:38PM +0100, Pawel Wielgus wrote:
>
>
> Ha! It works! But just after I exported this long variable inside VMD
> starting script. Anyway, so far looks stable, no problems.
>
> Neverthless I still would have a few questions...how can one draw a
> color scale-bar on the screen? And then adjust it (min and max values,
> choosing colors and so on...
> Any references?
>
>
> Thanks for help!
>
> Pawel
>
>
>
>
> John Stone wrote:
> > Pawel,
> > Did you verify that the system variable is being detected by VMD
> > at startup? What do your VMD startup messages say now? It could also
> > simply be a bug in 3-D (volumetric) texturing in the ATI driver. Does
> > color by "Volume" work for you, or does that similarly produced a solid
> > black object? With VMD 1.8.5, the VolumeSlice representation should be
> > relatively insensitive to various driver bugs because texture coordinates
> > are explicitly calculated for the vertices of the VolumeSlice plane, so
> > as long as the video driver does its job, I would expect you to see a
> > correctly textured slide plane. If you change the background color
> > to white, do you see a black slice plane, or do you see nothing at all?
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Mon, Mar 12, 2007 at 09:00:45AM +0100, Pawel Wielgus wrote:
> >
> >>Dear John,
> >>
> >>after exporting the system variable, I can see sth like this:
> >>
> >>Info) File loading in progress, please wait.
> >>Info) Using plugin cube for structure file test.cube
> >>cubeplugin) trying to read cube data set 0
> >>Info) Analyzing Volume...
> >>Info) Grid size: 80x80x80 (7 MB)
> >>Info) Total voxels: 512000
> >>Info) Min: 0.000000 Max: 0.706192 Range: 0.706192
> >>Info) Computing volume gradient map for smooth shading
> >>Info) Added volume data, name=test.cube : Gaussian Cube: kom density=scf
> >>Info) Using plugin cube for coordinates from file test.cube
> >>Info) Determining bond structure from distance search ...
> >>Info) Finished with coordinate file test.cube.
> >>
> >>Looks not bad. But that's all. I still can't see anything on my screen
> >>when the VolumeSlice representation is chosen :(
> >>
> >>
> >>Pawel
> >>
> >>
> >>
> >>John Stone wrote:
> >>
> >>>Pawel,
> >>> Ah, I see the issue. Well, you have a choice of either force-enabling
> >>>full rendering functionality (and risking crashes due to a number of
> >>>known ATI driver bugs that are to my knowledge still not fixed based
> >>>on recent reports from others), or using a different machine or a different
> >>>video card. If you wish to take your chances with the ATI video driver
> >>>and tell VMD to enable all rendering features, you can do this by
> >>>setting the environment variable VMDDISABLEATILINUXWORKAROUND, like this:
> >>> setenv VMDDISABLEATILINUXWORKAROUND 1
> >>>
> >>>After setting that environment variable, you should be able to start
> >>>VMD again, but without the functionality limitations imposed by default
> >>>when an ATI Linux driver is detected. Do not be surprised if you manage
> >>>to crash VMD, the X server, or even lockup your machine, as I've seen all
> >>>of these situations occur with both the open source and ATI provided
> >>>drivers for Linux. Oddly, the same hardware works fine with the ATI
> >>>provided Windows driver, so I think this is mainly an issue with their
> >>>Linux driver series.
> >>>
> >>>If you're able to use VMD reliably with full features with your ATI
> >>>Linux driver I would be very interested to hear about it, as many other
> >>>ATI users have encountered stability problems when using the advanced OpenGL
> >>>rendering features. Any tips that help others with their ATI drivers
> >>>are appreciated.
> >>>
> >>>If you have stability problems when full functionality is enabled I would
> >>>report this to ATI on their support forums. If you don't get a response
> >>>from them, then it may be time to consider getting a different video card
> >>>if working with volumetric data is important to you.
> >>>
> >>> John Stone
> >>> vmd_at_ks.uiuc.edu
> >>>
> >>>On Fri, Mar 09, 2007 at 04:54:26PM +0100, Pawel Wielgus wrote:
> >>>
> >>>
> >>>>Thanks for your reply.
> >>>>When my VMD starts, one can read:
> >>>>
> >>>>Info) ATI Linux driver detected, limiting features to avoid driver bugs.
> >>>>Info) OpenGL renderer: MOBILITY RADEON X300 Generic
> >>>>Info) Features: STENCIL MDE CVA MTX PP PS GLSL(OVF)
> >>>>Info) GLSL rendering mode is NOT available.
> >>>>Info) Textures: 2-D (2048x2048), 3-D (2048x2048x2048), Multitexture (8)
> >>>>
> >>>>I really don't know what 'limiting features' mean. What I know for sure
> >>>>is that I really had lots of troubles when compiling ATI fglrx drivers.
> >>>>And I did it finally only against 2.6.10 kernel. But that's a long story...
> >>>>
> >>>>What do you think? Any special features in fglrx configuration needed ?
> >>>>
> >>>>
> >>>>Pawel
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>John Stone wrote:
> >>>>
> >>>>
> >>>>>Pawel,
> >>>>> Yes, the VolumeSlice representation has been available for some time
> >>>>>and should work fine so long as you have a video card that supports
> >>>>>3-D (volumetric) texturing. You can check this by reading the VMD OpenGL
> >>>>>related startup messages. You should see a texturing info line like
> >>>>>the one I've pasted below:
> >>>>> Info) OpenGL renderer: ZFB, VIS
> >>>>> Info) Features: STENCIL MSAA(16) MDE MTX GAS
> >>>>> Info) Textures: 2-D (4096x4096), 3-D (512x512x512), Multitexture (4)
> >>>>>
> >>>>>The important part of that status line is: "3-D (512x512x512)"
> >>>>>
> >>>>>What video chipset are you using? Have you checked to make sure
> >>>>>that you're using the latest video driver available for your hardware?
> >>>>>
> >>>>> John Stone
> >>>>> vmd_at_ks.uiuc.edu
> >>>>>
> >>>>>On Fri, Mar 09, 2007 at 04:27:17PM +0100, Pawel Wielgus wrote:
> >>>>>
> >>>>>
> >>>>>
> >>>>>>Dear VMD Users,
> >>>>>>
> >>>>>>may I ask you a question concerning the visualization of volumetric data?
> >>>>>>I have a simple example of density for CH4 (just for graphical testing)
> >>>>>>in a Gaussian03 cube format. The volumetric data is read properly, and
> >>>>>>using 'Drawing method = Isosurface' I can easily get the density.
> >>>>>>
> >>>>>>But as only I switch to 'Drawing method = VolumeSlice' everything
> >>>>>>disapears. As far as I know the volume slices (along cartesian axis) are
> >>>>>>possible with VMD-1.8.5.
> >>>>>>
> >>>>>>What wrong am I doing ? Should I switch any options on ? Could you give
> >>>>>>me any hint?
> >>>>>>
> >>>>>>
> >>>>>>Regards
> >>>>>>
> >>>>>>
> >>>>>>Pawel Wielgus
> >>>>>>
> >>>>>>
> >>>>>
> >>>>>
> >
> 

-- 
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