I have read the answer you gave to simran jeet about residues in disallowed
position, sugesting to build multiple models and pick the best one. Your
answer conducts me to the following question. How to build multiple models,
with multiple templates or performing several models with the same template
and selecting that with the lowest objetive value? In this case, how many
models are indicated to run?
A second doubt I have is about validation. As the tutorial indictes, one
should check the log file from the modeling run for runtime errors
(`model-single.log') and restraint violations. I did it but I do not know
how to interpretate the restrain violations. Can anyone help me to
interpretate them? .I have also run the file `evaluate_model.py' to
evaluate my model with the DOPE potential, but I do not know how to access
to gnuplot. Finally I'd like to check the model with procheck_NT but
something is wrong with the pdb file. Anyone knows other rasonable way to
validate the model, preferebly a web site to perform the analysis on line.
Thank you very much,