[Chimera-users] Chimera-users Digest, Vol 55, Issue 29 (heightmaps)

Jonathan Hilmer jkhilmer at gmail.com
Thu Nov 29 14:21:46 PST 2007

I would also be interested to learn how to do heightmaps in Chimera,
or if it would be possible to add such a feature.  Right now we use
ImageJ (which doesn't have enough functionality) and Blender (which
has too much), while Chimera would be perfect.

In response to Gabe's question, it's not terribly convenient but you
could use the Zone tool to generate just the 'positive' region and
save that as a unique file.  The 'combine.py' could then be used to
subtract out the positive from the original, leaving the zeroed parent
density file.


> Message: 1
> Date: Wed, 28 Nov 2007 22:12:40 -0800
> From: "Gang 'Gary' Ren" <gren at msg.ucsf.edu>
> Subject: [Chimera-users] 2D for 3D display
> To: chimera-users at cgl.ucsf.edu
> Message-ID: <web-5552878 at msg.ucsf.edu>
> Content-Type: text/plain; charset="ISO-8859-1"; format="flowed"
> Hi, Chimera,
> I wonder how to create the 3D display by using the 2D
> image as below?
> http://www.cgl.ucsf.edu/chimera/ImageGallery/entries/afm/stmv-afm-large.png
> best regards
> Gary
> ----------------
> Gang Ren, Ph.D.
> Phone: (415) 476-8284;  Fax: (415) 514-2550
> Email: gren at msg.ucsf.edu; Web: 3dem.ucsf.edu
> Department of Biochemistry & Biophysics
> 1700, 4th Street, Byers Hall (QB3), room 301C
> San Francisco, CA 94143-2532
> ------------------------------
> Message: 2
> Date: Thu, 29 Nov 2007 10:23:49 -0800
> From: Thomas Goddard <goddard at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] reverse "zone" tool?
> To: Gabriel Lander <glander at scripps.edu>
> Cc: 'Chimera BB' <chimera-users at cgl.ucsf.edu>
> Message-ID: <474F03B5.5060609 at cgl.ucsf.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> Gabriel Lander wrote:
> > Hi Tom,
> > is it possible to somehow make the "zone" tool in the volume viewer do
> > the reverse of what it does?  I have a PDB docked into a density file
> > and I want to remove the density surrounding it so that it's easier to
> > focus on the rest of the structure.
> > By the way, I thoroughly enjoyed your demo of the new Chimera features
> > here at the cryo course, I'm sorry I didn't have a chance to chat very
> > much afterwards,
> > Cheers,
> > -gabe
> >
> Hi Gabe,
>    One trick would be to use the "Color Zone" tool to color the surface
> near the fit model completely transparent (hence invisible).  Use menu
> entry Actions / Color / From Editor, click the Opacity button and set
> opacity to zero.  Your molecule will be invisible.  Then use Tools /
> Volume Data / Color Zone, select all atoms (Select / Select All) and
> press the color zone dialog Color button.  Then go back and change the
> color of the molecule to something visible.
>    Three drawbacks of this approach.  First, it doesn't allow you to
> save the map with the region near the molecule zeroed out -- it is only
> coloring the surface.  Second, having a partially transparent surface
> makes the rendering slower.  Third, Chimera only handles one transparent
> model correctly.  If you try to add a second transparent surface you
> will see odd effects, like the invisible patch blocks the second
> transparent surface.  If these limitations are severe, I can give you a
> bit of Python code that actually makes a copy of the map with the part
> near the molecule erased.
>         Tom
> ------------------------------

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