Hello!
I am working on a project that involves programmatically specifying bonds, and would like to visualize the results. Will iRASPA read bonds out of a .cif file, or are the inferred bonds the only option? Sorry if this is RTFM, and thanks in advance.
No, the bonds are not read, and dynamically recomputed. VMD can read the bonds from file I think (without recomputing them).