[modeller_usage] Loop refining

Hi modeller users

I've already modeled a structure of an OBP (insect proteins). I picked the structure (pdb) with the lowest DOPE score, which is actually has the best stereochemical quality according to Procheck. After that, I used the script for "loop refining" in a positive range of values according to Anolea (showed as red bars). I was waiting a better stereochemical quality after the loop refinement, however, more bad contacts among residues and low allowed positions were obtained. My question is, What aspects must I take into consideration for loop refinement?, Is possible that the modeled structure do not need any loop refining?

Best regards

Herbert

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Herbert Venthur Peña
Profesor de Estado en Ciencias con Mención en Química

Estudiante de Doctorado en Ciencias de Recursos Naturales

Laboratorio de Ecología Química
Universidad de La Frontera
Temuco, Chile

08-3104992