VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Nov 20 2020 - 12:58:14 CST

Hi Lothar,
  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,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Nov 20, 2020 at 01:30:57PM -0500, Lothar Esser wrote:
> Hi,
> 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 apbs.in file can
> be run on the commandline with apbs 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
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/