@ I sent this help letter before but no response.I hope some one could help me out of trouble.

@ I am I do not know how to get the alignment file even after i read through the tutorial. It seems that if you have a @ template (preferred PDB code) and target seqeunce, and the alignment file in PIR format, you could run homology @ modeling. Am I rignt ?

@ If i know the sequence of targets and template , what should i do next ?

/* *# Homology modelling by the MODELLER TOP routine 'model'.

*INCLUDE # Include the predefined TOP routines (like c languange include <math.h>)

*SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file *SET ALNFILE = 'alignment.ali' # alignment filename (where the pre-aligned file, "alignment.ali" come *from?) *SET KNOWNS = '5fd1' # codes of the templates *SET SEQUENCE = '1fdx' # code of the target *SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom files *SET STARTING_MODEL= 1 # index of the first model *SET ENDING_MODEL = 1 # index of the last model * # (determines how many models to calculate)

*CALL ROUTINE = 'model' # do homology modelling */