I have been having some problems superimposing generated models on top of my template coordinance. I have used SET FINAL_MALIGN3D = 1 command in my top file but not *_fit files were given. This is puzzling to me since using the same top script for a different modeling job worked well and *_fit files were generated. Let me say that I am very new to Modeller, and script driven software in general, and for that reason would greatly appreciate if somebody could explain to me why *_fit files were not created. Moreover, I would be very grateful if somebody could provide me with the script that could be used for the purpose of superimposing .B999000* onto the template file after top script has been executed. Thanks in advance,
ps: This is my model.top file:
# Homology modelling by the MODELLER TOP routine 'model'.
INCLUDE # Include the predefined TOP routines
SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file SET ALNFILE = 'align.ali' # alignment filename SET KNOWNS = 't1b1' # codes of the templates SET SEQUENCE = 't3b1' # code of the target SET ATOM_FILES_DIRECTORY = '' # directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 30 # index of the last model # (determines how many models to calculate)
SET MD_LEVEL = 'refine_3' # defalt is 1; 5 is very slow with MD anne. SET FINAL_MALIGN3D = 1 # superimposis template and resulting pdb SET LIBRARY_SCHEDULE = 1 SET REPEAT_OPTIMIZATION = 10 SET RSTRS_REFINED = 2 SET MD_RETURN = 'FINAL'
CALL ROUTINE = 'model' # do homology modelling