Dear Warren, Thanks for the message and thanks for the pymol program. It is one of the most interesting programs that I worked with.
I tried to make all of the atoms in the waters HETATM, and after all of the records of the atoms, I put CONECT for all of the water molecules. In the Win version, I could not 'see' a mistake. But there are so many waters that I am not 100% sure. However, in the Linux version I installed, (I am on the process of making the program out of the source myself, but I am not very sure which make rule I should use. I am trying Rules.linux-rpm-rh72-py21n right now.) pymol does not connect any of the water molecules. All of the oxygen and hydrogen atoms are not connected to anything. I hope that I can get some breakthrough myself. Of course I will be glad if you can check my pdb files for me but I prepared so many different versions and I am not sure which version should I send you. I will do that if I still could not get out of it. Thanks again. Regards, K.K.Liang
