VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Mar 11 2005 - 17:17:37 CST

Hi,
  At the present time there's no way to modulate transparency
by the volumetric data values. I'm currently working on writing
GLSL shaders for volume rendering, and this is something that might
fit into that code however. It's a good idea, I just don't have a
nice way of implementing this in standard OpenGL for various reasons.
I'll see if I can implement this in the GLSL shader I write.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Mar 09, 2005 at 03:58:32PM -0700, YAMAZAKI Takeshi wrote:
> Hello John,
>
> Thanks for your reply.
> Now I can change colors using active color scale as you mentioned.
>
> However, I think I couldn't let you know what I had wanted to ask you
> fully.
> So, please let me try to ask you once again.
> I am so sorry for disturbing you many times.
>
> What I really wanted to ask you was, is it possible to draw nothing
> (real transparence) according to a certain value in volumetric data in
> the volume slice representation?
> Just in case, I am attaching my figure (myvolumeslice.tga) to make my
> question clear.
>
> This contour plot shows a distribution of water molecules around this
> large molecule.
> The darker region represents lower distribution and the brighter shows
> higher distribution.
> In this distribution, the value 0.00 means there is no water molecule
> around this molecule and the value 1.00 means the distribution of water
> around this molecule is just like bulk water.
> What I am really interested in here is the values except 0.00 and 1.00.
> Therefore, if I can draw this volumeslice not using values of 0.00 and
> 1.00, and if those regions which have 0.00 and 1.00 values are really
> transparent (not transparent material), it would be great help for me.
>
> If this is not clear enough, please let me know.
> I am so sorry for disturbing you many times, again.
>
> Please let me know if this is possible or not, when you are free.
> Thank you so much for your help.
>
> Takeshi
>

>
>
>
>
>
> On 2005/03/06, at 20:36, John Stone wrote:
>
> >
> >Hi,
> > You can use the "color by volume" method to override the normal
> >coloring of the VolumeSlice representation. From there, you can
> >set the "color scale data range" settings in the trajectory tab,
> >which will use the active color scale.
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Fri, Mar 04, 2005 at 05:26:33PM -0700, YAMAZAKI Takeshi wrote:
> >>Hi all,
> >>
> >>Is it possible to change coloring way in a volume slice
> >>representation?
> >>If it is possible to assign a color to a certain value by user,
> >>for example 0.000 is white and 1.000 is black (if "transparence" can
> >>be
> >>chosen instead of black color in this case, it would be nicer for me),
> >>it would be great help for me.
> >>
> >>Any help will be appreciated,
> >>Thank you in advance.
> >>
> >>Takeshi
> >
> >--
> >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
> >
> >
> YAMAZAKI, Takeshi, Dr.
> Postdoctoral Fellow
>
> National Institute for Nanotechnology
> National Research Council Canada
> W5-077, 5th Floor, ECERF Bldg., University of Alberta
> 9107-116 Street, Edmonton, AB T6G 2V4
> Canada
>
> Tel: (780) 492-8694
> Fax: (780) 492-8632
> E-mail: takeshi_at_ualberta.ca 

-- 
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