I understand now, I was only taking into account Ca-Ca distances for which the mathematical from was a Gaussian but if I use multiple templates the restraint becomes multimodal and the from is a spline. If I were to plot the distances with a gaussian from I would be plotting the probability density and the distance values. What are the values that I get for the spline?

Thank you.



From: Modeller Caretaker <modeller-care@salilab.org>
Sent: Thursday, April 16, 2020 7:09:15 PM
To: Mariana GONZALEZ MEDINA; modeller_usage@salilab.org
Subject: Re: [modeller_usage] Ca-Ca restraints
On 4/16/20 8:41 AM, Mariana GONZALEZ MEDINA wrote:
> I have observed that the more templates I include in the homology
> modeling the least Ca-Ca distance restraints I obtain. I can't
> understand this since I would expect to obtain restraints from missing
> residues, homology, etc from more templates and therefore more
> restraints imposed into my model. What could an explanation to this?

A given CA-CA distance will only have a single restraint on it,
regardless of how many templates you have (although it will become
multimodal). (If Modeller were simply to add restraints for each
template you would end up with a model that is an average of all
templates, which is not physically correct - if one template says a
CA-CA distance is 10A and another says it is 20A, the distance in the
model should be either 10A or 20A, not 15A.)

        Ben Webb, Modeller Caretaker
modeller-care@salilab.org             https://salilab.org/modeller/
Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage