Dear Knut J, Please don't use DOPE as such to evaluate model. NEVER USE DOPE ALONE TO RANK MODELS. ONLY DOPE IS NOT A GOOD SELECTION MEASURE. Use normalized_dope or GDT to rank models/Clusters/Hybrid Models.
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1. Re: Structural alignment using iterative_structural_alignment (Modeller Caretaker) 2. about model rank (albert) 3. Regarding Salign (Ashish Runthala) 4. Re: about model rank (Knut J Bjuland)
Message: 1 Date: Fri, 25 Feb 2011 16:04:47 -0800 From: Modeller Caretaker email@example.com Subject: Re: [modeller_usage] Structural alignment using iterative_structural_alignment To: Seungyeul Yoo firstname.lastname@example.org Cc: email@example.com Message-ID: 4D68439F.firstname.lastname@example.org Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 2/25/11 9:48 AM, Seungyeul Yoo wrote: > I was trying to clean two pdb files and superpose them based on the > pairwise structural alignment. ... > But when I replaced it to > 'modeller.salign.iterative_structural_align(aln), I had error message like:
My best guess is that every combination of parameters failed for the first loop, so it has no alignment to refine. If you can send me your full inputs (which two PDBs are you trying to align?) I'll see if it can be fixed.
Ben Webb, Modeller Caretaker
On 3/1/11 12:23 AM, Ashish Runthala wrote: > NEVER USE DOPE ALONE TO RANK MODELS. ONLY DOPE IS NOT A GOOD SELECTION MEASURE.
Such a strong statement needs to be backed up by a publication... particularly given that it is contradicted by both your next sentence and our own study (Prot Sci 17, 1881-1893, 2008).
> Use normalized_dope
Normalized DOPE is derived from the raw DOPE score. Thus the ranking of models, given the same sequence, will be the same with DOPE or normalized DOPE.
However, since raw DOPE is an "energy", you should certainly not use it to rank models that differ in sequence. For that, normalized DOPE would be more appropriate.
> or GDT to rank models/Clusters/Hybrid Models.
GDT is a structural measure, like RMSD, so it requires another structure to compare against. This makes it useless for assessing comparative models unless you already know the answer (as in CASP).
Ben Webb, Modeller Caretaker