I really appreciate the features that Chimera has (as I read them in yhe user's guide). 
Though there seem to be a problem:

I want to match two small molecules (and in the future maybe more), but If I open the pdb files in Chimera and use the command line match, it says that there is missing an atom spec.

Then I looked again in the user's guide and I noticed the "#" that they use. 

I don't know how what this "#" means. I just want to overlap the two structures and get a percentage of homology or something like that. That would be great.

You can always contact me,

kind regards,