On 02/13/2010 03:12 AM, Ashish Runthala wrote: > How do i consider the following analysis during the modeler run > itself like assess.dope, assess.GA341 etc in model-mult.py etc. > 1. Z score as Modeler doesn't reach below 1 in z scores.

Normalized DOPE Z scores are typically the most reliable method of model assessment.

> 2. RMSD to the template structure with just one template considered.

This doesn't make a whole lot of sense, since Modeller always builds models that are structurally similar to the template. This will simply give you a score that strongly correlates with the sequence identity.

> 3. GDT-TS scores etc.

Sure, if you have the known (native) structure, one benchmark is to compare the model against the native using the GDT-TS score.

You can add additional assessment methods to automodel by simply writing a Python function and adding that Python function to the assess_methods list in the automodel constructor. For example, the GA341 assessment method simply looks like:

def GA341(atmsel): """Returns the GA341 score of the given model.""" mdl = atmsel.get_model() return ('GA341 score', mdl.assess_ga341())

> And to modeler caretaker, i have something to share with you. How to > go about that.

You can find contact details on our website: http://salilab.org/modeller/contact.html

Ben Webb, Modeller Caretaker