Bala Murugan wrote:
I am new to this list and to modeller too. I was wondering that anybody faces the problem connected with max_pdf error. I have submitted modeller a job to model a protein of around 1200 residues. In the log it says that, >>summary of failed models 1fdx.B999900001.PDB obj.func. (109595.656) exceeded max_molpdf (100000.000).I don't know what is meant by max_molpdf. How should i proceed from this point?
max_molpdf is a maximum value for the objective function, used to discard really bad models. See http://salilab.org/modeller/8v2/manual/node44.html You can increase it by setting a.max_molpdf before you call a.make(), but this error is usually an indication of your initial model being very poor. You should examine the .ini file; perhaps your templates are not well aligned.
Ben Webb, Modeller Caretaker
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