Dear Dwey, You can use “Join Models” to join any structures that are open as two separate models (from two separate input files). You just couldn’t use the “peptide” option in that tool if they are not peptides; you would have to use the “other bond” option. See the Join Models part of the Build Structure tool for details: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.ht...> You are more likely to find answers to questions in the User’s Guide than in the chimera-users archive. You can search the User’s Guide with menu: Help… Search Documentation. If that doesn’t help, then emailing the forum (CC’d here) is recommended unless you are including private data. 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 Nov 9, 2015, at 2:05 PM, MPI <mpi566@gmail.com> wrote:

Dear Elaine Thanks for kindly answering my questions in Chimera forum.

I have a question related to compounds and I appreciate your valuable oppions.

Let's say I have compound A and compund B. Both have strucctures.

I would like to use a moiety (part) of compound A and a moeity (part) of compound B. I wonder if Chimera can combine the desired moeities of compound A and compound B to generate a new compound C.

Another simpler version. Can Cimera merge compound A and compound B into compound D ?

I checked Chimera list but I found that Chimera provides a function of joining models NOT for "compounds/drugs" but rather for "Proteins". I also see you made comments in the past. I wonder if you can provide insights into "compounds" or some hints to allow me working on compounds in Chimera. Many thanks, Dwey