VMD-L Mailing List

From: Samuel Coulbourn Flores (scflores_at_stanford.edu)
Date: Tue Apr 01 2008 - 13:25:08 CDT

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