VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Apr 25 2006 - 10:49:28 CDT

Nathan,
  The initial implementation I wrote doesn't autoscale, it
uses the selected field multiplicatively with the user-selected ribbon
width parameters. This works great for doing things with scripts, but
leaves something to be desired as far as arbitrary width modulation from
any of the per-atom data fields. Do you want a binary with this feature
turned on? Now that I'm back from travelling I can make binaries with this
feature enabled...

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Apr 21, 2006 at 01:08:00PM -0700, Nathan C. Rockwell wrote:
> John,
>
> Thanks for the quick reply. Incidentally, I have a nonstandard use for the
> variable width (using it to represent homology information rather than,
> e.g., NMR ensembles), which is why I was interested in how it was
> implemented. If, for example, it doesn't autoscale or take signed input,
> then I need to be able to set up input such that it will be happy.
>
> Thanks again,
> nr
>
>
> On 4/21/06 12:52 PM, "John Stone" <johns_at_ks.uiuc.edu> wrote:
>
> > Nathan,
> > The color by volume feature still misbehaves on MacOS X due to 3-D
> > texturing issues on that platform. The feature isn't disabled, but until
> > the Mac drivers work correctly, it'll continue be unusable. (or until
> > I find a way to work around the problem by changing VMD, if Apple doesn't
> > fix the driver) Several other people have told me that they are also having
> > problems with 3-D texturing on MacOS X, so this is apparently not specific
> > to VMD.
> >
> > The ribbons width modulation feature is still non-production, so in order
> > to enable it, you'll have to compile from source or get a binary from me.
> > I hope to get it into the GUI for the next version.
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >
> > On Fri, Apr 21, 2006 at 12:32:16PM -0700, Nathan C. Rockwell wrote:
> >> Hi all,
> >>
> >> just wondering whether a couple of things that have been discussed on VMD-L
> >> have been resolved in 1.8.4.
> >>
> >> 1. Has color-by-volume become possible for PowerPC Macs? I know it's not
> >> running on my machine with 1.8.4, but I was curious as to whether that was
> >> still expected or not. Last I heard, Apple was still trying to figure out
> >> the problem.
> >>
> >> 2. Is the variable width for NewRibbons available in the 1.8.4 download?
> >> This was discussed on the list about a month ago as a fairly early test
> >> version, and I can't tell whether it was included in 1.8.4 or not.
> >>
> >> 3. Also, related to 2, how is the variable radius implemented? Does it
> >> autoscale off of the actual range of B or occupancy values? Could it handle
> >> signed input values?
> >>
> >> Thanks,
> >> nr
> >> 

-- 
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
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