Hi all, just a short question to make sure if: the assess_dope method in MODELLER accounts for all atoms when calculating the dope energy profile for each residue?
(if so, do you know/think if DOPE may be more accurate than PROSA to some extent since the latter once take into account of the Calpha and/or Cb potential only)
Thanks for answering. Good day/night!
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hori koshii wrote: > Hi all, just a short question to make sure if: > the assess_dope method in MODELLER accounts for all atoms when > calculating the dope energy profile for each residue?
DOPE is calculated for all heavy atoms. See modlb/atmcls-mf.lib for the defined atom types, and for more detail the DOPE publication: http://salilab.org/pdf/174_SheSalProtSc2006.pdf
Ben Webb, Modeller Caretaker
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hori koshii
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Modeller Caretaker