Re: [modeller_usage] DOPE and sequence/model length
To: Starr Hazard <>
Subject: Re: [modeller_usage] DOPE and sequence/model length
From: Modeller Caretaker <>
Date: Mon, 20 Dec 2010 17:01:01 -0800
Cc:
On 12/16/2010 11:51 AM, Starr Hazard wrote:
This is several questions I guess. 1) Are DOPE energies normally
distributed? Could I statistically compare DOPE scores of models made
with one template to those from another template.
DOPE is a sum of individual energies over all pairs of atoms in your
final model - it does not include any information from the template or
modeling process. So you can compare DOPE scores for two models of the
same sequence, regardless of their source.
2) I have some evidence that longer XY pairs have "better" DOPE
scores than shorter pairs. Is there a statistical way to control for
"length"?
You can't compare these directly. Use the normalized DOPE score instead,
which *is* corrected for length (it is a z score).
3) I was just looking at DOPE scores for two models. One with from an
alignment with gaps and the other from an alignment without gaps.
The PDB model files are different sizes yet the scores are identical.
Does DOPE ignore regions that are not in the template?