Re: [IMP-users] problems with a sample script (basic IMP optimization)
To: Help and discussion for users of IMP <>
Subject: Re: [IMP-users] problems with a sample script (basic IMP optimization)
From: Daniel Russel <>
Date: Wed, 28 Jul 2010 16:37:24 -0700
Reply-to: Help and discussion for users of IMP <>
On Jul 28, 2010, at 9:09 AM, Benjamin SCHWARZ wrote:
>> As Ben pointed out, you can use RestraintSets to weight things. This does get to a more fundamental problem that weighting inhomogeneous restraints relative to one another is fundamentally broken and should be avoided. We are working on solutions to that (using an inference based optimizer Keren developed), but for now you have to fool around with weights.
>
> Just to be 100% sure to understand : what you mean when saying this approach is "broken" is that rather a technical / software problem, it is a fundamental / theoretical evilness / badness to mix "things" that do not leave in the same space. Though, since a more theoretically justified technique is not yet at hand, a weighted sum of restraints will do the trick.
The latter. It is a fundamental problem, rather than a software problem. Different restraints have different minima, grown to different values and at different rates. As a result there isn't really a set of weights that makes sense over a whole optimization process.
>
> Concerning Keren's development, has it got anything to do with Domino ?
Yes, We are working on a version (domino2) which is based on filtering of possible conformations based on the scores of individual restraints.
--Daniel