Yun He wrote: > Hi, everybody. The structures produced by MODELLER are stored in PDB format, > what does the value in last column stand for? In a normal PDB file, there is > a temperature factor column, but in the modeller structure, it is not like a > temperature factor, what is it?

Normally in an automodel run, model.energy() is called with output='LONG VIOLATIONS_PROFILE'. This writes out the per-residue violations of all restraints into a .V file, and also into the temperature factor (Biso) column of your PDB. See http://salilab.org/modeller/manual/node151.html

You can also call model.write_data() to calculate other properties and write them into the Biso column. See http://salilab.org/modeller/manual/node141.html

Ben Webb, Modeller Caretaker