VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Mar 11 2011 - 12:37:14 CST

Hi Jun,
  The Tachyon (and indeed POV-Ray and others) will show you your bond
lengths in the VMD 1.9 beta version. If you get a garbled PPM file
when using the snapshot capture from the OpenGL window, then the likely
cause is your graphics driver. If you are using Ubuntu and you have
the desktop special effects (Compiz / Composite) turned on, that may
be the cause of your problem, as they are known to interfere with normal
OpenGL, particularly in the case of stereoscopic display and other advanced
OpenGL features. If you have a test scene that triggers the degenerate
cylinder problem with POV-Ray, send me the structure file and VMD saved
state that goes with it, and I will see if it can be avoided or not.

Cheers,
  John

On Fri, Mar 11, 2011 at 06:26:13PM +0000, Jun Cheng wrote:
> Thanks, John.
> I used the graphical interface for vmd movie plugin, and tried all the
> rendering modes. All of them failed to make a movie I need, as
> explained in my original post. Perhaps tachyon is better than the
> others, with a flaw of not showing bond lengths.
> I will follow Axel's suggestion to try the VMD 1.9 beta to see what I
> can get. Finger crossed!
> Cheers,
> Jun
>
> On Fri, Mar 11, 2011 at 4:31 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> > Jun,
> >  Jacob is referring to the "snapshot" rendering mode that is built into
> > VMD.  VMD can eiether capture images from its own OpenGL window and use those
> > to make the movies ("snapshot" mode), or you can use high quality ray tracing
> > packages like Tachyon, POV-Ray, and others to make the movies, by selecting
> > the rendering mode in the graphical interface for the VMD Movie plugin.
> >
> > Cheers,
> >  John Stone
> >  vmd_at_ks.uiuc.edu
> >
> >
> > On Fri, Mar 11, 2011 at 03:36:49PM +0000, Jun Cheng wrote:
> >> Thanks, Jacob.
> >> I have ppmtompg installed. But I only know how to take screenshot,
> >> haven't heard of recording a video on screen. Is screencapture a
> >> software being able to do this?
> >> Cheers,
> >> Jun
> >>
> >> On Fri, Mar 11, 2011 at 3:20 PM, Goldsmith, Jacob <jgoldsmith_at_uky.edu> wrote:
> >> > I use Linux to make movies in VMD.  Generally I use screencapture and ppmtompg (might need to download this plug-in).  See if that works.
> >> >
> >> > -Jacob
> >> > ________________________________________
> >> > From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] On Behalf Of Axel Kohlmeyer [akohlmey_at_gmail.com]
> >> > Sent: Friday, March 11, 2011 6:58 AM
> >> > To: Jun Cheng
> >> > Cc: vmd-l_at_ks.uiuc.edu
> >> > Subject: Re: vmd-l: problem on making a movie
> >> >
> >> > On Fri, Mar 11, 2011 at 5:42 AM, Jun Cheng <chengjunw_at_gmail.com> wrote:
> >> >> Hi all,
> >> >> I am trying to use vmd movie generator to make a movie to visualize a
> >> >> MD trajectory. I have tried different renderers without success so
> >> >> far.
> >> >> I first used snapshot, and got garbled .ppm images, probably because
> >> >> of the problem Linux OpenGL video drivers (My OS is ubuntu), as
> >> >> explained in the vmdmovie webpage.
> >> >> Then, I installed povray, and ended up with the error: Parse error:
> >> >> degenerate cylinder, base point = apex point, which is apparently a
> >> >> very old problem after digging in the mailing list. This leaves me the
> >> >> only hope, tachyon. I do get a movie at the end after a long wait.
> >> >> However, the bond length labels (I intend to monitor the bond lengths
> >> >> changing along the MD run) are mysteriously missing.
> >> >> Can anyone help me here? Many thanks in advance
> >> >
> >> > try the latest VMD 1.9 beta instead.
> >> >
> >> > axel
> >> >
> >> >> Jun
> >> >>
> >> >
> >> >
> >> >
> >> > --
> >> > Dr. Axel Kohlmeyer
> >> > akohlmey_at_gmail.com  http://goo.gl/1wk0
> >> >
> >> > Institute for Computational Molecular Science
> >> > Temple University, Philadelphia PA, USA.
> >> >
> >> >
> >
> > --
> > 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