[modeller_usage] mutate_model on protein with ligand

[Anna Marabotti <>]

Dear Modeller caretaker,
I used mutate_model.py to introduce a single point mutation into the 
structure of my protein with a ligand bound into the active site. The 
mutation I introduced was near the ligand, and when I had a look at the 
resulting structure, I saw that the mutated residue has been located in 
too strict proximity with the ligand (i.e. the mutated residue and the 
ligand collide with each other). My suspicion is that this script does 
not take into account the presence of ligands or other elements marked 
as HETATM in the original protein. Is this true? In order to encompass 
this problem, if this is true, can I simply replace HETATM with ATOM  in 
order to make mutate_model.py correctly functioning?
Many thanks in advance and best regards
Anna Marabotti

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______________________________________________
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

"Indifference is the eighth deadly sin" (don Andrea Gallo)