harpreet singh wrote: > I am running energy command in modeller with the parameters > very_log, violations_profile and energy_profile > > in the log file I am getting very few violations in the "summary or > restraints violations" , but when i see the the violations profile file > the number of violations listed in this file are much more as compared > to the violations mentioned in summary. > > Can you please help me understanding why there is duifference in > violations shown in summary and that listed in the violations profile.

The violations profile file does not list the "number of violations". It lists the heavy relative violation of each _residue_, as defined at http://salilab.org/modeller/9v2/manual/node99.html

The log file lists the number of _restraints_ with a heavy relative violation greater than the cutoff in the NUMVI column (see http://salilab.org/modeller/9v2/manual/node243.html)

Even if the two quantities were the same, you wouldn't be able to compare the violations file directly with the log file because the violations profile may also be normalized and/or smoothed in the same way as energy profiles, as discussed at http://salilab.org/archives/modeller_usage/2007/msg00239.html

Ben Webb, Modeller Caretaker