Dear pymolers, I have to study the outcome from our MD calculations on a protein surrounded by about 1700 water molecules. There are 12000 such PDB files, each for one specific moment of time.
Now the problem is, when I tried to load some of the PDB files into a movie, pymol will link the water molecules wrongly. Some oxygen atoms are linked to more than two hydrogens. What's more, I tested the data both on the Windows version and the LINUX (redhat) version (both are the latest just downloaded and installed last Thursday), there are many more mistakes in the LINUX version than in the Windows version, although both versions make mistakes. I dig out the test data file of water (water.pdb) from the package, which uses HETATM instead of ATOM for the atom records, and again I tried it on both versions. This time, there is no mistakes in the Windows version, but still there are several mistakes in the LINUX version. I was wondering whether there is anything we can do to prevent pymol from linking the atoms wildly? In my datafile, there are TER records after the protein and after each molecule. I also tried to add CONNECT records for waters, but these do not provent pymol from making extra links. It will be highly appreciated if you have any concrete suggestion. K.K.Liang
