Hi there. I have been able to perform the basics of building a homology model and have a few questions about improving it.
I built the model with the top script below: ------------------------------------------------------------------------- INCLUDE # Include the predefined TOP routines
SET ALNFILE = '1frp+1fbp+Prgn.ali' # alignment filename SET KNOWNS = '1frpA 1fbpA' # codes of the templates SET SEQUENCE = 'Prgn' # 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 = 1 # index of the last model # (determines how many models to calculate) SET HETATM_IO = 'on'
CALL ROUTINE = 'model' # do homology modelling ------------------------------------------------------------------------
The structures 1frpA and 1fbpA are the same, and they contain hetero atoms. I haven't been able to use the hetero atoms as restraints and transfer them to the homology model using BLK or "." Can I do this with a slight modification to this script?
What exactly is the meaning behind setting "STARTING_MODEL" and "ENDING_MODEL"? Does setting the former to 1 and the latter to, say, 7 result in seven models being built with the 7th model being the most refined?
I'm not clear on how to refine a model. Without providing any other constraints other than what is provided by the structures and hetero atoms, is this straightforward to do by augmenting the above script?
Thanks, Christian Barrett