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
> 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: azat@salilab.org - WWW/URL: http://salilab.org/~azat
> > 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)
Well, the problem is that I don't really understand how to do this from what the manual says.
Christian
Hi Azat (and all)
Q: How do I obtain the manual (FAQ)? I have not downloaded the software yet. Regards, Dave Soriano U-Pittsburgh- Bradford in Pa.
David Soriano wrote: > > Hi Azat (and all) > > Q: How do I obtain the manual (FAQ)? I have not downloaded the software > yet. Regards, Dave Soriano U-Pittsburgh- Bradford in Pa. > >
manual: http://salilab.org/modeller/manual/ FAQ: http://salilab.org/modeller/manual/node114.html
-- - 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: azat@salilab.org - WWW/URL: http://salilab.org/~azat
> > Q: How do I obtain the manual (FAQ)? I have not downloaded the software > yet. Regards, Dave Soriano U-Pittsburgh- Bradford in Pa.
A web version or downloadable postscript is available from http://salilab.org/modeller/modeller.html
Christian
participants (3)
-
Azat Badretdinov -
Christian Barrett -
David Soriano