VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Dec 31 2020 - 13:44:41 CST

Lothar,
  I have tracked down the issue you have been having with your
VMD electrostatic coloring. It seems that there is a bug that occurs
with MSMS surfaces in combination with color by Volume.
I was able to reproduce the problem you described locally.

I find that if I switch the surface method to one of the other types,
such as Surf, QuickSurf, or Nanoshaper, the problem goes away.
I'm surprised that this is happening. It is a latent bug
that has surfaced over time since this had been working fine for
many years. I believe it has to do with ACTC triangle strip surface
optimization which is unique to MSMS presently. I found that if I render
the MSMS surface as a wireframe, even that works correctly. This
is further evidence that the problem has something to do with ACTC
surface mesh optimization.

For the time being, I suggest that you try Surf, QuickSurf, or NanoShaper
(or MSMS in wireframe) and I will have to debug what is happening here.

I will also add a user-override method for disabling ACTC in the
future, in case any other ACTC related issues should arise down the road.

Best regards,
  John Stone

On Fri, Nov 20, 2020 at 02:52:23PM -0500, Lothar Esser wrote:
> Hi, John,
> Â thanks for your super fast reply. A few days ago, I had a sent a very
> detailed account of the problem to [1]vmd_at_ks.uiuc.edu but never heard a
> thing. In the meantime I did make some progress. It seems you are saying
> tachyon should render colored surfaces and only in my unusual case(s) it
> seems to fail. The example that I provided back then is simply crambin (I
> have a much more complicated molecule but here crambin 1crn.pdb failed
> already).
> BTW I think you are probably right: The new APBS required a version of gcc
> that I did not have and had to compile. One library ended up in
> LD_LIBRARY_PATH.
> Okay, I am attaching one example. The my_vmdscene.tga is what Tachyon
> produces for me.
> Thanks,
> Lothar
> Â
> On Fri, Nov 20, 2020 at 1:58 PM John Stone <[2]johns_at_ks.uiuc.edu> wrote:
>
> Hi Lothar,
> Â APBSRun tries to locate APBS using your default command
> search path, as it exists when VMD is launched. Since APBS
> may depend on shared libraries set in LD_LIBRARY_PATH, there's
> an extra potential complexity, because recent Linux distros
> have decided to clear out LD_LIBRARY_PATH for shell child
> processes as a (in my view bizarre) form of extra security.
> The upshot of this is that if you require a special setting of
> LD_LIBRARY_PATH for ABPS, that may be the source of the problem
> and not its inclusion in the default command search path.
>
> Regarding your difficulty with Tachyon, if you can provide
> me with a test case that reproduces the behavior your describe,
> that would be the best way forward. Although it "works for me",
> you may have found a strange case where my code is misbehaving.
>
> I would want a tar.gz archive containing the electrostatic map,
> your VMD saved state file, and the exact "render" command you
> ran to generate the image(s) that are problematic. If you're
> using the GUI to launch Tachyon, you can use the "logfile console"
> command to get VMD to tell you what render command it is running
> in response to your mouse actions.
>
> Best regards,
> Â John Stone
> Â [3]vmd_at_ks.uiuc.edu
>
> On Fri, Nov 20, 2020 at 01:30:57PM -0500, Lothar Esser wrote:
> > Hi,
> >Â Â because of the excellent visual representation of surfaces when
> ambient
> > occlusion is used, I am planning to render a surface with
> electrostatic
> > potential in Tachyon (in-memory). However, tachyon only produces black
> and
> > white surfaces. That is in contrast to colored surfaces say colored by
> atom
> > types. So this is surprising.
> > I am using 1.9.4a48 on CentOS7.
> >
> > Also, I noticed that whenever I use ambient occlusion, regardless of
> > whether I turn on or off Shadows in Graphic options, it renders the
> scene
> > *with* shadows. Previous versions of vmd did not do that as far as I
> > remember.
> >
> > A smaller side issue is that vmd does not execute APBS even though it
> is in
> > the path. After running APBS (local) it displays immediately: APBSRun:
> > output files missing or unreadable.
> > Obviously it does not even try to execute it. However the [4]apbs.in
> file can
> > be run on the commandline with apbs [5]apbs.in and the pot.dx file
> copied to
> > the working directory.
> > Not that important but, if someone knows whether this is a permission
> issue
> > or something else, I would like to know how to fix it.
> >
> > The major issue for me is that Tachyon does not render surfaces
> colored by
> > (APBS) electrostatic potential and to a much lesser degree the problem
> that
> > shadows are always on even when they are turned off.
> >
> > Any advice is appreciated.
> >
> > Lothar
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> [6]http://www.ks.uiuc.edu/~johns/Â Â Â Â Â Â Phone: 217-244-3349
> [7]http://www.ks.uiuc.edu/Research/vmd/Â Â Â
>
> References
>
> Visible links
> 1. mailto:vmd_at_ks.uiuc.edu
> 2. mailto:johns_at_ks.uiuc.edu
> 3. mailto:vmd_at_ks.uiuc.edu
> 4. http://apbs.in/
> 5. http://apbs.in/
> 6. http://www.ks.uiuc.edu/~johns/
> 7. http://www.ks.uiuc.edu/Research/vmd/ 

-- 
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/