Hi Francesco, It only means that whatever file(s) you are reading into Chimera do not specify the bond explicitly. I can't tell from the information given whether your MD program knows the bond is there; it may know, but not write this information into the file that you input to Chimera. If the file(s) describe trajectory in the format of the MD program (AMBER? GROMOS?) and you are using the MD Movie tool in Chimera for display, all the bonds should be there. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.ht...
However, if you are doing something else like writing a PDB file from those programs, maybe the PDB file does not specify the bond explicitly, and the other viewers might have a more relaxed criterion for automatically identifying a bond. I don't think there is a way to change the automatic criteria, but you could just add a CONECT record specifying the bond to the PDB file, or just add the bond in Chimera with the command "bond" or the "Add/ Delete Bonds" section of Build Structure. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/bond.html> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.htm...
Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Nov 16, 2008, at 11:00 AM, Francesco Pietra wrote:
For a monochlorinated small alkaloid docked onto a protein model, after molecular dynamics simulations Chimera shows the chlorine atom as a dot, without a line to represent the bond. Before dynamics, the C-Cl line connecting the two atoms was shown. Other viewers show the bond both before and after MD. For the purpose of presentation, how to set a longer C-Cl bond length as a temporary default for Chimera?
Very likely the parameterization for chlorine in the MD suite is not as it should.
Thanks francesco pietra