[Chimera-users] Draw user specified object

[Elaine Meng]

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