Dear, 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, Jo Sourbron PhD Student Laboratory for Molecular Biodiscovery Department of Pharmaceutical and Pharmacological Sciences Katholieke Universiteit Leuven O&N2, Campus Gasthuisberg Herestraat 49, box 824 B-3000 Leuven, Belgium j.sourbron@gmail.com GSM. +32 474 94 84 17 TEL. +32 16 37 78 07 http://be.linkedin.com/pub/jo-sourbron/33/496/77a/