From: Kassem Ghaddar (
Date: Tue Jan 05 2010 - 04:09:16 CST


i have encountered a Problem after adding an molecule to an already exiting model created in VMD. When i save the coordinates of this molecule, the new cartoon representation shows only one alpha strand of the molecule (atoms 1 to 14) followed by the molecule that i added (tryptophan 601). it seems that the new model calculates the position of the C (alpha) atoms and apparently the position of the molecule that i added is closer to the carbon 14 than the normal C 15 that should follow. the other representations show the whole molecule, but still include my new molecule in the backbone of the chain, even though i precise in the PDB file that it should be considered as a separate chain.

Where does the rest of my molecule disappear in the New Cartoon mode ?

thank you

PHD student
Structure et Fonction des Membranes biologiques (SFMB)-Brussels
Molecular Physiology of the Cell-Gosselies