Hi Miguel,
First, congratulations for using bioinformatic...
With your script, you will generate 5 models. I think it not enough.
Basically, modeler generates models and attributes for each one what we
call an 'objectiv function', which corresponds approxymately to the energy
of the model (constraints included). So, the more models you will
generate, the more you will have a chance to choose the model with a very
low energy.
Moreover, it seems that the mutation you want to test is in a
loop. So, under modeller, you can use another function, which uses a
better scoring function for modelling (you find it in last pages of the
documentation).
I hope this will help you.
Good luck,
Mickael Krzeminski
On Fri, 23 Jul 2004, Miguel Relloso-Cereceda wrote:
> Dear Modeler mailing list,
>
> I am a user of MODELLER 6v2 for Linux, and I am using this program to
> model the mutations that I am making on CD1b. I am looking for new
> interactions between amino acids that could be generated by these
> mutations and for possible changes generated in loops. This is the
> modeller that I am using:
>
> INCLUDE
> SET ATOM_FILES_DIRECTORY = '/home/moodyb/Miguel/37t/'
> SET OUTPUT_CONTROL = 1 1 1 1 1
> #SET PDB_EXT = '.pdb'
> #SET MD_LEVEL = 'refine1'
> SET STARTING_MODEL = 1
> SET ENDING_MODEL = 5
> #SET DEVIATION = 4.0
> SET KNOWNS = 'CD1b'
> #SET HETATM_IO = off
> #SET WATER_IO = off
> #SET HYDROGEN_IO = off
>
> #SET ALIGNMENT_FORMAT = 'PIR'
> SET SEQUENCE = 'CD1b-37t'
> SET ALNFILE = '37t.pir'
> CALL ROUTINE = 'model'
>
> Are these parameters the best way to get my objectives? I do not have much
> experience in computer science, and I went through your manual and I did
> not understand it at all. Please contact me with any advice and if it is
> not convenient, could you tell me who might be able to help me?
>
> Thank you very much.
>
> Miguel Relloso.
>
>
>
> ----------------------oOO-(_)-OOo----------------
> Miguel Relloso Ph.D.
> Brigham & Women's Hospital
> Harvard Medical School
> Smith 514
> 1 Jimmy Fund Way
> Boston, MA 02115
> phone: 617.525.1027
> fax: 617.525.1010
>
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