Hi all, I am refining a protein structure with phenix and COOT, and COOT worked fine for three runs. The pdb file is composed of two protein chains, two ligand chains, and a water chain. Suddenly at the last run the pdb file opened by COOT only has chain A, while the same file opened by Pymol contains all the chains. Does anyone know how to solve the problem? I am using Mac OS 10.6.8 system, and the COOT version is 0.7. I have tried to uninstall and install it several times with two installation files (one from the CCP4 website, the other from a link on phenix documentation), and it does not help.
Thanks! Jing
