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