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model building questions



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