VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Mar 15 2011 - 14:14:04 CDT

Jun,
  I'll have to look into why your label offset didn't work
as expected in Tachyon/POV-Ray, if it's not yet incorporated in
those cases, then it should be trivial for me to fix it.

Regarding the graphics driver and behavior you were seeing with
the Snapshot renderer, yes, that's unusual. Did you make sure to
prevent the screen saver from activating while making your movie?
You would also need to ensure that you don't move any windows over
the top of the VMD OpenGL window while making the movie when using
the Snapshot renderer. Either of those two things could also create
problems depending on the particular graphics driver you're using.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Mar 15, 2011 at 01:42:09PM +0000, Jun Cheng wrote:
> Hi John,
> Sorry for the late reply.
> I installed the 1.9 beta version. Tachyon indeed shows the bond
> lengths. However, several bond labels overlap with each other even
> though the positions have been adjusted using label_property panel.
> POV-ray has the same problem. I guess this should be easy to fix in
> the later version.
> After playing a bit with draw settings, I probably find the cause of
> the error about degenerate cylinder with POV-ray. What I am really
> trying to do is to visualize some spin density change in a MD
> trajectory (a series of .cube files). When drawing the isosurface with
> wireframe, I get the error. If removing the isosurface or switching it
> to solid surface, it works fine. So I think isosurface with wireframe
> is the problem.
> Back to snapshot, it works better than 1.8.7 version, however not
> perfect. I usually get most of correct .ppm files, but some snapshots
> are essentially the same, as the movie is frozen for a while.
> Fortunately, I ran twice of movie making, and the freezing occurs at
> different times so that I can combine them to get a series of correct
> .ppm files, from which I make the movie I need. This is probably
> because of my graphics driver or some settings of Ubuntu, as you
> suggested. But I am not going to investigate it further at this point.
> It will be very helpful if it is possible to make VMD work better with
> Tachyon and POV-ray.
> Many thanks,
> Jun
>
> On Fri, Mar 11, 2011 at 6:37 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
> > 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
> > 

-- 
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