I'm Enrico Ronca a post-doc researcher at the National Research Council of Italy in Perugia.

I'm contacting you because I often work with metal atoms and not always chimera show me bonds.

I solved the problem removing all bonds and pseudo bonds and adding "reasonable bond between selected atoms" in the adjust bonds menu of chimera.

Is there a way to run the same procedure from the command line so that I could automate it by a script?

Thank you in advance for your reply.

I'm looking forward to hearing from you

Enrico