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@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 ----- 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