Annalisa, If bonds are not explicitly provided in the input file, then PyMOL infers bonding based on distance. Are the input coordinates valid? It looks like the atoms may be too close together in space... Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com
_____ From: annalisa bordogna [mailto:annalisa.bordo...@gmail.com] Sent: Thursday, December 18, 2008 6:40 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] weird visualization of a peptide structure Hi all, I have a little problem with the visualization of a peptide conformation: as you can see from the picture I enclose, the structure appears as if every atom is bound to every neighbour atom. What (and how) can I set in PyMOL, to visualize a correct structure? Thank you very much for your help. Best regards, Annalisa ------------------------------------------------------- Annalisa Bordogna Ph.D. Student Università degli Studi di Milano - Bicocca Milano, IT
