Adriana Esteves wrote: > 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?
Certainly if you have multiple possible templates, there may be some value in trying each of them (or a combination). But by "multiple models" we usually mean to build many models for the same template.
There is no rule on how many models to build, but if your models show a lot of variation in energy or structure, you probably need to build more to get adequate sampling.
> 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?
Generally speaking if a 'strong' restraint (such as distance) is violated by more than 2 or 3 standard deviations, it's worth investigating. Weaker restraints such as phi-psi are probably less of an issue.
> 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.
You don't have to use gnuplot. Any program which can plot the value in the rightmost column in the text file output by evaluate_model.py will do. For example, Excel works just fine too.
> Finally I'd like to check the model with procheck_NT but > something is wrong with the pdb file.
Many validation tools are designed for X-ray structures, and so will reject theoretical models, since they don't have things like required REMARK lines and experimentally reasonable temperature factors.
Ben Webb, Modeller Caretaker