To: Christian Barrett <>, modeller_usage <modeller_usage>
Subject: Re: model building questions
From: Azat Badretdinov <azat>
Date: Tue, 09 Jun 1998 16:03:30 -0400
Organization: Rockefeller University
> 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