VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Apr 01 2008 - 13:37:18 CDT

Sam,
  Can you post a copy of the movie you're having problems with
on a web page somewhere for me to take a look at?

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Apr 01, 2008 at 11:25:08AM -0700, Samuel Coulbourn Flores wrote:
> I'm using Apple's QuickTime Player, Version 7.4.1 (14)
>
> The trajectory doesn't look jumpy in VMD, although of course the
> playback is slowed down significantly by the movie maker program. Is
> it possible for the frames rendered to disk to get out of sync with
> the frames displayed in the viewer window? Or is are they explicitly
> tied together in the code?
>
> I tried a trajectory step size of 10 rather than 1 but this didn't fix
> the problem.
>
> Sam
>
> On Apr 1, 2008, at 10:53 AM, John Stone wrote:
>
> >
> >Hi,
> > I've never seen the sort of symptoms you describe. What software
> >are you using to play the resulting MPEG movie? Do you see this
> >"jumpy"
> >behavior when you animate the trajectory within VMD itself, or is this
> >problem unique to the resulting MPEG movie? When you made the MPEG
> >movie, did you make sure to disable your screen saver so that nothing
> >was interfering with the VMD OpenGL rendering while the movie was
> >being recorded?
> >
> >Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >
> >
> >On Tue, Apr 01, 2008 at 10:38:47AM -0700, Samuel Coulbourn Flores
> >wrote:
> >>Hi Guys,
> >>
> >>I'm trying to make a movie out of an NMR-format pdb file with 1500
> >>frames, displaying the motion of an RNA with 30 residues. I render
> >>using 'licorice' drawing style, color by atom name, and start the
> >>movie maker application. The movie duration is 25 seconds, all other
> >>settings are the default ones. The resulting mpg is jumpy,
> >>repeatedly
> >>stalling on a single frame for a second or so before jumping and
> >>catching up. Also some frames show the molecule rendered in blue
> >>rather than the full colors. I tried shutting down other
> >>applications, thinking VMD was competing for CPU time with other
> >>applications. However the problem remains. I have a dual core
> >>MacBook Pro, so hardware shouldn't be an issue. Can anyone tell me
> >>what I might be doing wrong?
> >>
> >>Many thanks
> >>
> >>Sam
> >>
> >>
> >>On Apr 1, 2008, at 4:06 AM, Axel Kohlmeyer wrote:
> >>
> >>>On Tue, 1 Apr 2008, Ben Chern wrote:
> >>>
> >>>BC> Axel,
> >>>BC> Thanks for you advice.
> >>>BC> I'll try to compile the source under linux.
> >>>
> >>>ben,
> >>>
> >>>you still have not satisfied my curiosity!
> >>>what are you planning to change, once you
> >>>get VMD compiled? i am very curious to learn
> >>>what it is you have in mind, that cannot be
> >>>done in scripting, perhaps with the help of
> >>>a little plugin...
> >>>
> >>>cheers,
> >>> axel.
> >>>
> >>>
> >>>
> >>>BC>
> >>>BC> On Tue, Apr 1, 2008 at 10:47 AM, Axel Kohlmeyer
> >>><akohlmey_at_cmm.chem.upenn.edu >
> >>>BC> wrote:
> >>>BC>
> >>>BC> > On Tue, 1 Apr 2008, Ben Chern wrote:
> >>>BC> >
> >>>BC> > BC> I want to show some chemical properties, e.g. bond energy,
> >>>but I would
> >>>BC> > not
> >>>BC> > BC> wish to do that using script.
> >>>BC> >
> >>>BC> > ben,
> >>>BC> >
> >>>BC> > "stupid question(TM)":
> >>>BC> > how do you plan to get those properties "into" VMD?
> >>>BC> > and how do you plan to visualize them, i.e. how are
> >>>BC> > they supposed to look like?
> >>>BC> >
> >>>BC> > before starting on a long and painful process where
> >>>BC> > you may at the end find out, that you won't get what
> >>>BC> > you planned, it may actually be a very good idea to
> >>>BC> > prototype what you want to do in scripting.
> >>>BC> >
> >>>BC> > this is how many of the features in VMD started (and
> >>>BC> > quite a few still are).
> >>>BC> >
> >>>BC> > BC> I have tried the CVS, but the error still exists.
> >>>BC> > BC> Would you please send me a tar file of the Windows build
> >>>area for VMD?
> >>>BC> >
> >>>BC> > also, have you considered using a linux/unix machine
> >>>BC> > for development? it is infinitely more convenient, the
> >>>BC> > way VMD "wants" to be built.
> >>>BC> >
> >>>BC> > just a few (curious) thoughts,
> >>>BC> >
> >>>BC> >
> >>>BC> > axel.
> >>>BC> >
> >>>BC> >
> >>>BC> > BC> Thank you very much.
> >>>BC> > BC>
> >>>BC> >
> >>>BC> > --
> >>>BC> >
> >>>=
> >>>=
> >>>=
> >>>====================================================================
> >>>BC> > Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu
> >>>http://www.cmm.upenn.edu
> >>>BC> > Center for Molecular Modeling -- University of
> >>>Pennsylvania
> >>>BC> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA
> >>>19104-6323
> >>>BC> > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel:
> >>>1-215-898-5425
> >>>BC> >
> >>>=
> >>>=
> >>>=
> >>>====================================================================
> >>>BC> > If you make something idiot-proof, the universe creates a
> >>>better idiot.
> >>>BC> >
> >>>BC>
> >>>BC>
> >>>BC>
> >>>BC>
> >>>
> >>>--
> >>>=
> >>>=
> >>>=
> >>>====================================================================
> >>>Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://
> >>>www.cmm.upenn.edu
> >>>Center for Molecular Modeling -- University of Pennsylvania
> >>>Department of Chemistry, 231 S.34th Street, Philadelphia, PA
> >>>19104-6323
> >>>tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel:
> >>>1-215-898-5425
> >>>=
> >>>=
> >>>=
> >>>====================================================================
> >>>If you make something idiot-proof, the universe creates a better
> >>>idiot.
> >>
> >>Samuel Coulbourn Flores
> >>Altman Lab
> >>Department of BioEngineering
> >>Stanford University
> >>650.644.8416
> >>
> >>サムエル　フロレス
> >>科学者
> >>生物工学部
> >>スタンフォ一ド大学
> >>スタンフォ一ド、カリフォルニア、米国
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >
> >--
> >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
>
> Samuel Coulbourn Flores
> Altman Lab
> Department of BioEngineering
> Stanford University
> 650.644.8416
>
> サムエル　フロレス
> 科学者
> 生物工学部
> スタンフォ一ド大学
> スタンフォ一ド、カリフォルニア、米国
>
>
>
>
>
>
>
>
>
>
>
>
> 

-- 
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