VMD-L Mailing List

From: Neda Rafieiolhosseini (ne.rafiee_at_googlemail.com)
Date: Mon Apr 27 2020 - 16:14:03 CDT

Thanks a lot for the information, John.
Bests,
Neda

On Mon, Apr 27, 2020, 11:04 PM John Stone <johns_at_ks.uiuc.edu> wrote:

> Hi,
> The Surf code is written in K&R C (not even early 90s ANSI C) and this
> has presented a problem for compiling the binary on MacOS X Catalina that
> I haven't resolved yet. Since we didn't write this code, I'm reticent to
> go and rewrite it all in a more modern-acceptable dialect of C. In the
> short
> term I would suggest using the QuickSurf representation instead. While the
> QuickSurf rep is a Gaussian surface rather than a solvent accessible
> surface,
> this is the best stopgap in the short-term until I come up with a way of
> building Surf with modern compilers. Straightforward things like trying to
> compile Surf with -std=c90 doesn't fly even with GCC due to the
> anachronistic
> C coding style and inconsistencies in Surf's function signatures and
> return types.
>
> Best,
> John
>
> On Mon, Apr 27, 2020 at 02:25:36PM -0600, Josh Vermaas wrote:
> > Surf depends on an external binary to work properly if I remember
> > correctly, and that binary may be caught up in the Catalina weirdness
> and
> > not run correctly, thereby generating no output. What happens if you
> > switch to QuickSurf? That one is implemented directly in VMD, so I'd
> > expect it to work more robustly.
> > -Josh
> > On Mon, Apr 27, 2020 at 12:25 PM Neda Rafieiolhosseini
> > <[1]ne.rafiee_at_googlemail.com> wrote:
> >
> > Dear All,
> > I have installed and used the latest version of VMD ([2]VMD
> 1.9.4a42 Rev
> > 3 for MacOS X CatalinaĀ (Apr 24, 2020)) on my system.Ā
> > I try to open a ".pqr" file of a protein and load a .dx file on top
> of
> > it to represent the surface charges on the protein. Everything is
> fine
> > until I set the drawing method to "Surf" and the coloring method to
> > "Volume" in Ā the graphical representation panel. The problem is
> that
> > when I set these two options, the protein in the OpenGL display
> > disappears giving thisĀ error:
> >
> > ERROR) Cannot read SURF output file: /tmp/vmdsurf.u501.268.in.tri
> >
> > Info) Done.
> >
> > I will be thankful if anyone can help with this.
> > Thanks.
> > Neda
> >
> > References
> >
> > Visible links
> > 1. mailto:ne.rafiee_at_googlemail.com
> > 2.
> http://www.ks.uiuc.edu/Research/vmd/alpha/vmd194a42-MacOSX-CatalinaOnly-Rev3.dmg
>
> --
> 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/
>