[modeller_usage] problem in using mutate_model.py

[Anna Marabotti <>]

Dear Modeller users,
I created several mutants of my protein (which is a homodimeric protein) 
using the script mutate_model.py.and all has gone perfectly, but I have 
a problem in introducing a mutation.

I want to introduce mutation in position 321 of both chains. So, I 
started introducing mutation in chain A using the command:
mod9.11 - myprot 321 TYR A <mutate_model.py> myprotTYR321.log
and all went OK. When I introduced the mutation in chain B starting from 
the mutant obtained in the previous step, using the command:
mod9.11 - myprotTYR321 321 TYR B <mutate_model.py> myprotTYR321TYR321.log
MODELLER gave me the following error message:
OverflowError:check_inf__E> Atom 5347 has out-of-range coordinates 
(usually infinity).
              The objective function can thus not be calculated.

The strange thing is that if I start introducing the mutation from chain 
B using the command:
mod9.11 - myprot 321 TYR B <mutate_model.py> myprotTYR321-B.log
MODELLER stops with the following error:
OverflowError:check_inf__E> Atom 5345 has out-of-range coordinates 
(usually infinity).
              The objective function can thus not be calculated.

I had a look at the original structure; atoms 5345 and 5347 are, 
respectively, atoms CB and O of the residue preceding the mutant one, 
and no apparent problems are present in the protein structure (no 
distortions, no aberrant structures - the residue is inserted into a 
beta sheet). But assuming that I have a problem on my structure, why the 
problem is not in the same atom when I start mutating from chain A or 
from chain B, considering that the procedure involves exactly the same 
residue?

Thanks a lot for your help, best regards
Anna

--
______________________________________________
Anna Marabotti, Ph.D.
Assistant Professor
Department of Chemistry and Biology
University of Salerno
Via Giovanni Paolo II, 132
84084 Fisciano (SA)
Italy
Phone: +39 089 969583
Fax: +39 089 969603
E-mail: 
Skype: annam1972
Web page: http://www.unisa.it/docenti/annamarabotti/index

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