[modeller_usage] Script for superimposing generated models

[Ivan Bosanac <>]

Hello All,

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,

Ivan

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