VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Dec 19 2007 - 20:59:02 CST

Oliver,
  I've posted two Linux builds with 64 bonds per atom in the alpha
directory in the VMD Public project on BioCoRE:
  http://www.ks.uiuc.edu/Research/vmd/alpha/

Give those a spin and let me know if all is well. I can do a MacOS build
for you tomorrow if the Linux builds work for you.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Dec 18, 2007 at 05:05:02PM -0500, Oliver Beckstein wrote:
> Hello John,
>
> > I can make you special builds with larger max bond counts.
>
> I appreciate this very much.
>
> >Will 30 be adequate? I can make it any number you like
> >up to 255, but the larger the number the more memory VMD will use
> >on a per-atom basis.
>
> To be on the safe side let's choose 64 – more are really not going to
> come up in my problems.
>
> Thank you,
> Oliver
>
> >
> >Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >
> >On Mon, Dec 17, 2007 at 02:37:42PM -0500, Oliver Beckstein wrote:
> >>Hello,
> >>
> >>is there a way to obtain binaries for Mac OS X and Linux i686 that
> >>have
> >>MAXATOMBONDS increased to, say, 30? I am (ab)using VMD for graph
> >>plotting and some of my nodes simply don't behave like atoms although
> >>I'd like to keep using atom-like representations instead of drawing
> >>bonds as graphics objects because it makes it so much easier to change
> >>colors, materials etc.
> >>
> >>As I understand it, MAXATOMBONDS is defined to be 12 in Atom.h:
> >>http://www.ks.uiuc.edu/Research/vmd/doxygen/Atom_8h.html
> >>
> >>I don't have the VMD source and as I understand it, it can be a bit
> >>complicated compiling it, though I'd give it a shot if this is too
> >>much
> >>work for the developers (which I would certainly understand).
> >>
> >>Thanks,
> >>Oliver
> >>
> >>--
> >>Oliver Beckstein * orbeckst_at_jhmi.edu
> >>
> >>Johns Hopkins University, School of Medicine
> >>Dept. of Physiology, Biophysics 206
> >>725 N. Wolfe St
> >>Baltimore, MD 21205, USA
> >>
> >>Tel.: +1 (410) 614-4435
> >
> >--
> >NIH Resource for Macromolecular Modeling and Bioinformatics
> >Beckman Institute for Advanced Science and Technology
> >University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> >Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> >
> >
> --
> Oliver Beckstein * orbeckst_at_jhmi.edu
>
> Johns Hopkins University, School of Medicine
> Dept. of Physiology, Biophysics 206
> 725 N. Wolfe St
> Baltimore, MD 21205, USA
>
> Tel.: +1 (410) 614-4435
>
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078