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. Jonathan

Message: 1 Date: Wed, 28 Nov 2007 22:12:40 -0800 From: "Gang 'Gary' Ren" <gren@msg.ucsf.edu> Subject: [Chimera-users] 2D for 3D display To: chimera-users@cgl.ucsf.edu Message-ID: <web-5552878@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@msg.ucsf.edu; Web: 3dem.ucsf.edu

Department of Biochemistry & Biophysics 1700, 4th Street, Byers Hall (QB3), room 301C San Francisco, CA 94143-2532

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Message: 2 Date: Thu, 29 Nov 2007 10:23:49 -0800 From: Thomas Goddard <goddard@cgl.ucsf.edu> Subject: Re: [Chimera-users] reverse "zone" tool? To: Gabriel Lander <glander@scripps.edu> Cc: 'Chimera BB' <chimera-users@cgl.ucsf.edu> Message-ID: <474F03B5.5060609@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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