VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 09 2002 - 14:05:23 CDT

Hi Holger,

On Thu, Jul 04, 2002 at 11:11:11AM -0500, Holger Frauenrath wrote:
>
> On Wednesday, July 3, 2002, at 02:47 PM, John Stone wrote:
>
> >Dear VMD-L,
> > Those of you that have been trying out the new native MacOS X
> >version may be interested to try a preliminary "bundle"-based
> >version
>
> First of all: thank you very much. This is great. And it seems to work
> well. Concerning the performance, I have the impression that it is already
> improved over v1.7 using X11. I have some small issues with VMD 1.8a16 on
> Mac OS X:
>
> * Can someone point me to some documentation or help files, in particular
> concerning the changes in the interface compared to v1.7? I have a number
> of stupid "howto" questions, and the VMD 1.8a17 documentation on the
> website still seems to describe the interface of v1.7 ... (I cannot find
> an obvious way to toggle the status of molecules in the list in the VMD
> window, or to delete molecules from the list, I wonder what primary and
> secondary files are for ... that kind of questions)

The state toggling in the new GUI is done by a popup menu accessed with
the right mouse button, or the meta key combinations on the Mac in some
versions of VMD 1.8, and in more recent versions we have put these
functions into the "edit" menu, though we may end up including them in
both popup and "edit" menu form depending on user feedback we receive.

> * Choosing the Help menu makes VMD look for Netscape, which it does not
> find (I haven't installed it)

This is something I have to work on still, as our Mac version doesn't really
know how to open web pages via the system yet.

> * I cannot load old pdb files generated with Chem3D. I figured that the
> reason is that they have Mac line endings (resaving them with unix line
> endings helps). Could you make VMD accept Mac line endings?

Can you send me an example file that has Mac line endings? If you can
send us an example, we should be able to fix that problem.

> And then I have one general question:
>
> * What are other people's recommendations on how to render files without
> using X11 apps? I found that rendering with Tachyon produces decent output
> in a readable file format. Are there other ways? Is there a way to use
> raster3d without X11 (I liked the renderings a lot)?

Most of the renderers (POV, Tachyon, Raster3D) can be built without X11
one way or another. The next pre-release version of VMD will come with a
new version of Tachyon that produces even better quality output by default,
and which supports perspective and orthographic projections, and
directional lighting that more closely matches what VMD does with OpenGL.

Let us know if you have other questions.

Thanks!
  John Stone
  vmd_at_ks.uiuc.edu 

-- 
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