VMD-L Mailing List

From: Jun Cheng (chengjunw_at_gmail.com)
Date: Tue Mar 15 2011 - 08:42:09 CDT

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
>