same issue already discussed some time ago, have a look at this topic: http://www.mail-archive.com/coot@jiscmail.ac.uk/msg01180.html
it would be nice if, when saving PDB files, coot would completely discard the CONECT lines. Best, Federico Forneris, PhD ------- Crystal and Structural Chemistry Bijvoet Center for Biomolecular Research - Utrecht University Padualaan 8 3584 CH UTRECHT - The Netherlands Tel. +31 (0) 30 253 2868 - Fax +31 (0) 30 253 3940 http://www.crystal.chem.uu.nl/group-gros/ -----Messaggio originale----- Da: Mailing list for users of COOT Crystallographic Software per conto di Heidi Schubert Inviato: ven 20-5-2011 23.54 A: COOT@JISCMAIL.AC.UK Oggetto: SSM Hi, Sometimes when I move a molecule using an SSM alignment the molecule looks fine in coot, but when saved and subsequently read into pymol has all kinds of problems. The problem is in the connect lines at the bottom of the file - if you remove them then pymol reads the file just fine. You could say that this is a pymol read problem, But I'm going to suggest that this is a coot write problem. These connect lines must mean something and whatever they mean it's not the same after you rotate the coordinates. So, maybe coot has to rewrite the connect files or leave them out? Heidi
