VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Dec 26 2005 - 11:59:43 CST

Hi,
  I'm still out of the office, but if you can send me a copy of the the
PDB file that exhibits trouble, I'll be happy to take a look. I didn't change
anything in VMD 1.8.4 that should affect the loading of multi-structure PDB
files as trajectories, but it's always possible that I created a bug while
making the significant changes I've made to the PDB reader recently.

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Dec 23, 2005 at 12:11:53PM +0800, h9826299_at_hkusua.hku.hk wrote:
> Dear John,
>
> I've found a problem in the VMD 1.8.4 beta 6 about loading of a molecule.
> I have a trajactory of 100 frames in pdb format. This file was loaded perfectly
> in VMD 1.8.3 as a 100 frame traj. However, it is loaded in the VMD 1.8.4 beta 6
> as a single molecule with all frames compressed into a ultra huge molecule.
>
> Is that the problem with my file or it's a bug?
>
> cheers,
> Chung
>
> >
> > Hi,
> > I've just done a fresh test build of VMD 1.8.4 beta 6 on all
> > of the platforms I'm currently able to compile on and I've posted
> > them on the web site for people to try out:
> > http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD
> >
> > I've also posted the current manuals for this test version here:
> > http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.4/docs.html
> >
> > To see the (large) list of changes since VMD 1.8.3, visit this page:
> > http://www.ks.uiuc.edu/Research/vmd/vmd-new/devel.html
> >
> > There are still several bugs I (and others) need to fix before this version
> > will become final, but this should now be very representative of what
> > it's going to look like. The main things I'm still working on are:
> > - Fix a few bugs with cartoon renderings of some unusual PDB files
> > - Update APBS plugin for the bleeding edge APBS version that was just
> > released (new config file syntax)
> > - Fix Python and TkInter problems (which affect usage of IED)
> > - Fix remaining bugs in the new movie maker plugin
> > - Finish last bits of the new STING plugin
> > - Fix remaining bugs in the new color scale bar plugin
> > - Finalize the shipping version of the new structure building plugins
> > - Documentation updates
> >
> > Enjoy,
> > 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
> >
>
>
> 

-- 
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