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[modeller_usage] Need Help with model accuracy

Hello all, 

I´m a begginer user of MODELLER, and I have a question for you: 
I´m making docking experiments, and the protein I have got from the PDB has some gaps, so the docking can´t go on. So, I thought I could model the protein using its own cristal as template. So I did,  but the models I got don´t fit very well with the original cristal (when I superimpose them with MacPyMol, the models are very deviated from the cristal). What can I do to improve the adjustment between models and template?

Thanks for your attention. 

Mª Victoria Ruiz Pérez 
CIBER de Enfermedades Raras 
Departamento de Biología Molecular y Bioquímica
 Facultad de Ciencias, Universidad de Málaga 
Campus de Teatinos, sn; 
29071 Málaga 
Tlf. 952 137135

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