[Chimera-users] Re: streaks in Chimera image of virus electron density map

Thomas Goddard goddard at cgl.ucsf.edu
Tue Oct 12 15:06:51 PDT 2004

Hi Lu,

  The streaks on your Chimera density map display are very likely a
driver bug specific to the Mac ATI Radeon 9600 Pro (RV350, 64 Mb).
You don't see the streaks on a Mac with Radeon 9600 XT graphics
(RV360, 128 Mb), and I don't see them with your data set on my
Mac Radeon 9800 Pro (R350, 128 Mb).  Setting the transparency to
a non-zero value makes the streaks go away.  When you use transparency
Chimera does not use OpenGL display lists.  This suggests that the
graphics driver bug is related to display lists.  OpenGL is an industry
standard 3D graphics library that Chimera uses.

  We have had alot of graphics driver problems with Apple.  We submit
bug reports to them and sometimes visit them in Cupertino, but it is
unlikely we could get this fixed since it appears to be limited to a
graphics card they no longer sell.

  If the streaks do not bother you on-screen too much, a reasonable
work-around might be to set transparency to 0.001 just when saving
an image.  This setting will substantially slow down rotation of the
model so it is best to leave the transparency at 0 until you get the
right orientation for image saving.

  Thanks for reporting the problem.


> Date: Tue, 12 Oct 2004 14:23:37 -0700
> From: Lu <lugan at scripps.edu>
> To: Thomas Goddard <goddard at cgl.ucsf.edu>
> Subject: Re: streaks in Chimera image of virus electron density map
> Hi Tom,
> I see definitely see streaks in the Chimera display, and they appear to be
> parallel to the one of the crystal lattices. They remain even if I rotate
> the particle. When I loaded a .pdb with axis coordinates, they appear
> parallel with the Y-axis. Another phenotype is that if I make the
> transparency non-zero, the streaks go away.
> The graphics card is an ATI Radeon 9600 Pro, 64mb. We don't notice this
> problem on our other G5, which has an ATI RV360 chip with 128MB of RAM. So
> there's a possibility that either our video card is bad, or that specific
> ATI model has some issues.
> I've attached an example map (which is a low resolution crystal structure
> by the way) of our virus particle. It's dsn6/omap formatted.
> I hope the problem is just isolated to our video card.
> Thanks.
> -Lu
> On Tue, 12 Oct 2004, Thomas Goddard wrote:
> > Hi Lu,
> >
> >   I took a look at the virus EM map image you sent to Eric Pettersen.
> > I haven't seen this bug in Chimera.  Do you see the streaks in the
> > Chimera graphics window?  Or do they only appear in the saved image?
> > If they appear in the graphics window are they features that persist
> > when the model is rotated?  Also are the streaks parallel the data set
> > x, y, or z axis?  You could see this by displaying the outline box
> > around the map with volume viewer / options / show outline box.
> >
> >   I have the same Mac as you only my RV350 has 128 Mb.  Do you happen
> > to know what model graphics card you have, for example, mine is Radeon
> > 9800 Pro?  I don't think you can find this out from Mac OS -- you just
> > have to know from when the machine was purchased.
> >
> >   I suspect our latest Chimera snapshot release 2029 that just came
> > out will exhibit the same problem.  But it might be worth trying it.
> >
> >   Can you reproduce the streaks with any small data set that I could
> > get from you (by web, ftp, or email)?
> >
> >   Hopefully we'll be able to figure this out quickly.
> >
> > 	Tom
> >

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