From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Feb 26 2007 - 16:41:14 CST

Hi,
  Can you tell me the exact sequence of steps you're performing, and
what program generated the original DCD file? Do you get the same behavior
if you save back out to another DCD file, or is this problem only associated
with formats such as XYZ etc?

  John

On Mon, Feb 26, 2007 at 05:28:41PM -0500, Nichols A. Romero wrote:
> Oops... I forgot to mention that those sequence of operations cause VMD to
> crash.
>
> On 2/26/07, Nichols A. Romero <naromero_at_gmail.com> wrote:
> >
> >Hi,
> >
> >I am reporting a bug in VMD 1.8.5. I am running RHEL on an Intel 32-bit
> >system. I also have nVIDIA video card
> >but I don't believe any of these details are relevant since I can
> >reproduce this problem on SGI Altix (IA64)
> >system as well which is quite different from my desktop machine.
> >
> >I am simply loading a Trajectory in DCD format and then trying to export
> >the coordinates to ANY format, e.g.
> >xyz, POSCAR, etc. I have run with the debug option and this is what I get.
> >
> >
> >(gdb) where
> >#0 0x0051b600 in strncpy () from /lib/tls/libc.so.6
> >#1 0x08142465 in MolFilePlugin::write_structure ()
> >#2 0x081020c7 in CoorPluginData::CoorPluginData ()
> >#3 0x0817219a in VMDApp::molecule_savetrajectory ()
> >#4 0x081b7186 in SaveTrajectoryFltkMenu::do_save ()
> >#5 0x083bde7c in Fl_Button::handle ()
> >#6 0x083ba310 in fl_throw_focus ()
> >#7 0x083ba402 in Fl::handle ()
> >#8 0x083cd057 in fl_handle ()
> >#9 0x083cc66e in Fl::remove_fd ()
> >#10 0x083cc890 in fl_wait ()
> >#11 0x083b9bb6 in Fl::wait ()
> >#12 0x0816e1fd in VMDApp::VMDupdate ()
> >#13 0x08184857 in main ()
> >
> >
> >
> >
> >
> >--
> >Nichols A. Romero, Ph.D.
> >1613 Denise Dr. Apt. D
> >Forest Hill, MD 21050
> >443-567-8328 (C)
> >410-306-0709 (O)
> >
>
>
>
> --
> Nichols A. Romero, Ph.D.
> 1613 Denise Dr. Apt. D
> Forest Hill, MD 21050
> 443-567-8328 (C)
> 410-306-0709 (O)

-- 
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