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Fri., Feb. 26th 2010 EBI Dear all, I've already replied privately to several people who replied when I first posted th question, but did not set the record-clear for the whole community and I do apologize. What I have is two or more 3D structures, not protein, similar in their 3D but equivalent atoms don't have the same atom-name. I thought that in order to rename equivalent atoms automatically I needed to 3D fit the two structures first. Adel Golovin of PDBeMOTIF fame (http://www.ebi.ac.uk/pdbe-site/pdbemotif) has pointed out that for the automatic atom renaming process all I needed was 2D-fitting via 2D-graph isomorphism routine which he could provide. Once all structures in a given set have the same atom names, 3D-fitting is doable using numerous software/utilities. Thanks again for the replies, especially to Pavel Afonine (phenix) with whom I had a lengthy exchange. CCP4-board is one of the best... Thanks again Miri