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Re: 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?

Yes, change the alignment as described in the manual (FAQ)

> 
> 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?


No, it does not. STARTING and ENDING will determine the range of indeces
in .B???? file names of the models

> 
> 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?

There are a couple of refinement TOP subroutines in __*.top files in
$MODINSTALL. (like 'refine' or 'model' which you used).

You can use them. Some of them are related to loops. Please look for
more information in the manual. 

Happy landings!

Azat.

--
- Dr. Azat Badretdinov 
- The Rockefeller Univ, Box 270 
- 1230 York Ave, New York NY 10021, USA
- Phone: (212) 327 7206
- Fax: (212) 327 7540
- E-mail: 
- WWW/URL: http://salilab.org/~azat