Hi there, I want to use Chimera on a server (or in an automated fashion by command line; "-nogui") to read in a bunch (1000s) of PDB structures (each having an identical number of atoms) and then do clustering using the NMRCLUST code that you've so conveniently adapted. I found this old thread: http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-October/003193.html Is this still the preferred method for doing what I'm hoping? Also, is it possible to do a MatchMaker alignment before the clustering? Thanks, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office 301-402-0095 Mobile 301-758-3559 http://bioinformatics.niaid.nih.gov<http://bioinformatics.niaid.nih.gov/> (Within NIH) http://exon.niaid.nih.gov<http://exon.niaid.nih.gov/> (Public) Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.