Raji Edayathumangalam wrote:
I have superimposed one structure on top of another. Now, I am interested in only displaying the water molecules that are identical between the two structures. MolA has ~3000 waters and molB has ~900 waters. There are ~330 water molecules identical between the two structures.
If none of the standard programs do it you could try: http://sb20.lbl.gov/berry/for/pdbdist3w.for write(6,*)'Read 2 .PDB files and list all pairs of atoms ' write(6,*) 'in one file within threshold distance' write(6,*) 'of atom in other file' write(6,*) 'create 2 new pdb files:' write(6,*) 'near.pdb contains all atoms in file1 within thresh' write(6,*) 'far.pdb contains all atoms in file1 outside thresh' It is dimensioned for 5000 atoms in file 1 right now, so it might be good to grep/awk all the waters from pdb file 1 into say waters1.pdb Then choose a threshold distance to decide which waters are identical, say 0.5 A pdbdist3w <<eof waters1.pdb pdb2.pdb 0.5 eof after it finishes near.pdb will contain all the atoms from pdb2.pdb that were within 0.5 A of an atom in pdb1.pdb- these should be your common waters. ed (Use at your own risk and don't blame me if you get the wrong answer, but this is so simple it couldn't be far wrong and it's always worked for me so far)
