Hanudatta Atreya wrote: > Should the residue-wise DOPE profile of the target modeled structure > necessarily match that of the template? This is because in the tutorial > online, the DOPE profile shown indeed follows very closely that of the > template.

No - since the profiles are derived from the DOPE energy, the absolute values cannot be compared between different structures. But you can qualitatively compare the rough shape of the profile between template and target to give a visual indication of your alignment quality (if the shapes are similar but shifted, your alignment probably is also shifted).

> In my case, the modeled structure has 1.0 Angstrom RMSD with the > template. However, the residue wise DOPE profile do not match with that > of template.

It makes no sense to compare your model with the template, because it will always be fairly similar by construction. And the DOPE profile, as explained above, is not conclusive.

> Also, other structure quality scores as I checked with > PROCHECK, MOLPROBITY etc. are poor. So does this indicate non-optimal > modeling? Especially the Clash-scores are high. Should I carry out one > more mimimization step myself to loosen the distortions?

If assessment methods indicate a poor model, by all means try to optimize it some more. But you may get better results by simply building more models and ranking them.

Ben Webb, Modeller Caretaker