Dear All I'm facing to problems with modeller. In the FAQ's question #16 there is an explanation on how to use hetero atoms in modelling adding the line HETATM_IO = on in the top script. There is also a comment (confuse in my opinion) about the use of w for water and . for other atoms in the alignment that still remains unsolved to me. In my case I'm trying to use FAD in the modelling. I can't wonder how to edit the alignment to include this Ws and .s Check the example given. INCLUDE SET ALIGNMENT_FILE = 'align1.ali', KNOWNS='templ1', SEQUENCE='targ1' SET HETATM_IO = on, WATER_IO = on CALL ROUTINE = 'model' The alignment file: >P1;templ1 structureX:templ1:1::10:: FAYVI/.wwww* >P1;targ1 sequence:targ1:1::8:: -GWIV/.ww-w* Need I to repeat the entire alignment (template/target) inside the same .pir file, but now only with signs like - , ., w , #) where the .s/Ws positions correpond to those aa that make contact with the HETATM in the structure/template ? The second question is about my log file. I'm habituated to use regularly Modeller since version 4 but suddenly the job was finished abruptly with this : MODELLER 6v2, 17 Feb 2002 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS assgn___544E> Variable name not recognized: /pipe1/databases/pdb/uncompressed_files/pdb1hci.ent Command line: INCLUDE assgn___525E> Error in TOP variable assignment. recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Is this some kind of bug or a user error ? I'm sure that the files are typed correctly (case-sensitive) and the folder where the job is started has all the files in it. Any hint asap will be very much appreciated. Thanks in advance brgds Frank Alarcon LNCC - Brasil www.lncc.br