[Chimera-users] Draw user specified object

Greg Couch gregc at cgl.ucsf.edu
Tue May 17 14:13:49 PDT 2005

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.


On Tue, 17 May 2005, Elaine Meng wrote:

> Date: Tue, 17 May 2005 14:00:55 -0700
> From: Elaine Meng <meng at cgl.ucsf.edu>
> To: Reza Khayat <rkhayat at scripps.edu>
> Cc: chimera-users at 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.html
> This tool just reads a text file with lines of the form
> atom1 atom2 color optional-label, e.g.
> #0:279.a at n #1:133.b at 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
> -----
> Elaine C. Meng, Ph.D.                          meng at 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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