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Re: [modeller_usage] weight restraints



On 5/27/10 6:49 AM, Armin Meier wrote:
I have a pir file with more than one template.
Each template has its distance restraints in the rsr-file.

Are you sure? That's not how Modeller builds restraints when using multiple templates. There should be a single restraint for each distance in the model; if you have multiple templates that restraint simply incorporates data from all of them.

How can I weight the distance restraints for each template individually,
i.e. all CA_CA-distance restraints for template t1 are weighted by a
factor w_t1, for template t2 w_t2 and so on, so that templates with
higher weight have more influence on the final structure.

You can't really, since it doesn't work that way. If you have two templates for a given distance, one of which has a distance of 5A and the other 10A, Modeller doesn't create two restraints on the distance, one at 5A and 10A, since that wouldn't work, of course - what you'd end up with would probably be a structure with a distance of 7.5A, which doesn't match either template. Instead, it combines the two observations into a single multi-modal restraint. See the 1993 JMB Modeller paper for the details.

If you really wanted to do it your way, you could run Modeller twice, once for each template, then combine the two restraint files using whatever scheme you like.

Rewriting the distance restraints and adding a weight as parameter maybe
is a solution

That seems unnecessarily complicated - you can simply reduce the standard deviation of a harmonic distance restraint to get the same effect as increasing the weight.

	Ben Webb, Modeller Caretaker
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