[chimerax-users] Question about the comparative homology modelling tool

[Elaine Meng]

Hi Tiglath,
These are questions that have no simple answers and require your own scientific judgment.

The number of models is a compromise.  More models will give you more choices and possibly find ones with better scores, but will take longer to calculate.  There is no one best number, as it completely depends on the details of your target and template, for what purpose you want to use the model.

No score is perfect.  All you can do is read about how each one is calculated to understand better what properties it represents (see explanations and paper citations at the Modeller website, links included in the ChimeraX documentation, see the "Modeller Results" section at the bottom of the page):
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html>

Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jan 12, 2021, at 1:03 PM, Moradkhan, Tiglath A <tmoradkhan at csus.edu> wrote:
> 
> Hi
> I have two questions about the homology modelling tool:
> 
> 	• Why is the default number of models to be built five? Does having five models provide a better choice for choosing the best model?
> 	• In evaluating a protein model which of the following parameters plays a much more dominating role: zDOPE, predicted RMSD or the predicted native overlap? Or do all three measures contribute the same effect on model evaluation? For instance a model might have a low zDOPE score but have a higher RMSD while another model might have a much more positive zDOPE score but a lower RMSD. Based on this, would the first model be the better one to pick or do both models have equal weight in terms of overall model quality? 
> 
> I would be very glad for advice.
> Thanks
> Tiglath