Hi,

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.

Best,

Mariana

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

> 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