Hello

I have been trying for some time now to model with 2 ligands and 1 water molecule and I feel that I have tried everything from the list, faq and tutorials and not got very far. I have posted a number of questions to the list but can still not get this to work, properly! I have managed to include the ligands and the water O into my output pdb by using the script and alignment below, however there is not recognition that this oxygen is a water and in the output model it is listed as BLK along with the other ligands. From reading posts in the user list I was expecting this water oxygen to be recognised as such, since i have used the w character to represent it and also HOH in the pdb file (the file has been edited to include only the protain, ligand and water that I am wishing to model around). I cannot type w at the end of the sequence alignment however as this causes modeller to fail with an out of range error. I would really appreciate some help as I have completelty exhaused all of my options now.

Thanks Jo

top INCLUDE SET ALNFILE = 'CcHh1-Bamu.pap', ALIGNMENT_FORMAT = 'PAP' SET KNOWNS = 'Bamu' SET SEQUENCE = 'CcHh1' SET STARTING_MODEL = 1 SET ENDING_MODEL = 1 SET HETATM_IO = on, WATER_IO = on CALL ROUTINE = 'model'

end of alignment (pap format) alignment _aln.pos 480 490 500 510 520 Bamu RKQLPEPDLTF/..w CcHh1 RNALPEPVIPA/...

produce model with water included as:

HETATM 4032 O BLK 525 37.988 89.184 33.629 1.00 25.09 2SG4034 END