VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed Jun 07 2006 - 07:01:03 CDT

On Wed, 7 Jun 2006, Come On wrote:

> Hi, all,

hi,

> First, thanks to Jone Stone's answer, and now I have got another two
> question in regarding to make the movie:
> 1) My system is protein in water, I want to represent the protein using CPK
> while the waters using points, I can do that by using creating rep. for a
> .pdb file, what I am asking is that how can I do that for a dl_poly HISTORY
> file, so that the movie i made will look much clear?

you can first load a .pdb file of your to get the stucture information,
then delete the corresponding coordinate frame and load the HISTORY
file 'into' the thusly created molecule. this is basically the same
as with .psf + .dcd combinations as shown in many tutorial examples,
but with the need to remove the coordinates associated with the .pdb.

> 2) I tried to use the movie maker for just export images, but can it
> captures only specified part of the screen instead of the whole screen?

no. you can either zoom in accordingly or post-process the rendered
images to show only the part of it. just look at how the postprocessing
is done in the moviemaker script using the netpbm utilities. you could
change that to use pnmcrop with the corresponding flags instead of
pnmsmooth and then just activate the 'smoothing'.

regards,
    axel.

>
> Thank you.
> Rachel
>
> On 6/6/06, John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> >
> > Hi,
> > 1) For "ball and stick" use the "CPK" drawing method in the graphical
> > representations menu. You may also like the "Licorice" mode.
> >
> > 2) The VMD movie maker currently only knows how to automatically drive
> > the VideoMach engine for making movies on Windows fully automatically.
> > On Unix machines (including MacOS X), the movie maker uses NetPBM, and
> > ImageMagick and other tools, but since these aren't available on
> > Windows,
> > we use VideoMach. The recent version of the movie maker plugin now
> > allows
> > you to just export a collection of images (no movie file per se), so
> > that you can use your favorite movie making tool (including ones that
> > aren't scriptable and require user interaction). That's probably the
> > best
> > way to go if you want to use a specific movie making package other than
> > VideoMach.
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Tue, Jun 06, 2006 at 07:11:55PM +0100, Come On wrote:
> > > Dear all,
> > >
> > > I want to make a movie from the HISTORY file generated by dl_poly, there
> > are
> > > two things I would like to ask:
> > >
> > > 1) can i view the atoms in the form of ball and stick ( which I can't
> > find
> > > from the display menu)?
> > >
> > > 2) is there any other softwares supported by VMD except the Videomach,
> > for
> > > example can i windows movie maker to do that?
> > >
> > > Thank you very much in advance.
> > >
> > > Best,
> > > Rachel
> >
> > --
> > 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
> >
> 

-- 
=======================================================================
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.