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:
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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
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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