Subject: [modeller_usage] DOPE profile of target structure
From: Hanudatta Atreya <>
Date: Mon, 17 Mar 2008 18:37:37 -0700 (PDT)
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.
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. 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?
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