Elaine Thanks for the tips but not successful. I checked some of the help sections, like select and atom specifier, and tried the command below Bond sel :88A@SG:96B@CA Msg received Mangled atom specifier! I tried the suggestion of using the Tools menu, but not evident how to do it. Is there a way to select more than one atom using cntrl and the mouse arrow. Thanks arthur -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: August-26-16 1:38 PM To: A G Szabo Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] bond formation Hi Arthur, If you just mean to draw a bond and not move anything, if the atoms are already selected you could just use command: bond sel <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/bond.html> There is also a graphical interface, Tools. Structure Editing. Build Structure, the Adjust Bonds section. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.h tml#bond> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Aug 26, 2016, at 7:14 AM, A G Szabo <agszabo@bell.net> wrote:
I am working with a PDB file that has two proteins docked together. As this is a model the two proteins do not have a bond between them. The model number is the same for the two chains designated A and B. I have looked through the various tutorials, functions and tools to figure out how to actually place a bond between two residues that link the two chains. It is well established as to how the two proteins would be linked if the bond had been formed. The linkage is between the S of a Cysteine and carbonyl carbon at the C-terminal of the other protein. I think I have managed to select both atoms, but cannot determine how to include a bond. Your assistance is appreciated. Arthur Szabo