VMD-L Mailing List

From: Samuel Coulbourn Flores (scflores_at_stanford.edu)
Date: Tue Apr 01 2008 - 12:38:47 CDT

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

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