Hi Reza,

Using the volume path tracer tool (menu Tools / Volumes / Volume Path Tracer) you can place marker spheres (actually atoms) with the mouse and link them with cylinders (actually bonds). It is intended for placing markers on high density regions of volume data. But you can use it without any volume data if you turn on the "Drop markers on empbyt space with mouse" option. Also you can move markers if you click on the "Move markers with mouse" option in the volume path tracer dialog. The spheres and cylinders can have whatever radii and colors you like.

The detailed documentation for this tools is in the Tools section of the Chimera User's Guide under Volume Path Tracer:

http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/vo...

You can show this documentation in a web browser by pressing the Help button on the volume path tracer dialog.

Tom

And one more possiblity, chimera can read in a VRML97 (aka VRML 2.0) file with arbitrary geometry in it and show that in conjunction with whatever else you're displaying. See http://www.web3d.org/x3d/vrml/index.html for details.

Greg

On Tue, 17 May 2005, Elaine Meng wrote:

Date: Tue, 17 May 2005 14:00:55 -0700 From: Elaine Meng meng@cgl.ucsf.edu To: Reza Khayat rkhayat@scripps.edu Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Draw user specified object

On Tuesday, May 17, 2005, at 12:53 PM, Reza Khayat wrote:

...

Hi, I was wondering if there is a way to draw a user specified object. For example, draw a cylinder (bond) from vertex x to vertex y. Thank you.

Hi Reza, We do not have a completely general approach to this, but there are a few different ways you could do it:

(1) if atoms are already at the endpoints, you can use the command "bond" to connect them; man page is http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/bond.html

However, you may not want to change the chemical nature of these atoms, bringing me to a second alternative

(2) if atoms are already at the ends, you can create pseudobonds to connect them using PseudoBond Reader http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pbreader/pbreader.h...

This tool just reads a text file with lines of the form atom1 atom2 color optional-label, e.g.

#0:279.a@n #1:133.b@n red

With these two options, you would have to already have atoms at the endpoints, which if not present in some structure, you could make by putting them in PDB format. However, the third option

(3) Volume Path Tracer (already described in Tom Goddard's mail) allows you to place the "atoms" interactively and then draw bonds. That is also the more flexible approach in terms of how the bond is displayed.

I hope this helps, Elaine

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Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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