VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Apr 27 2020 - 16:04:29 CDT

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 Catalina (Apr 24, 2020)) on my system.Â
> 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  the graphical representation panel. The problem is that
> when I set these two options, the protein in the OpenGL display
> disappears giving this 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/