daniel - sorry - this is an empty reply - pressed send my mistake. still figuring out how to summaries my thoughts on that .... ;) On Nov 1, 2009, at 1:43 PM, Keren Lasker wrote:
> > On Nov 1, 2009, at 11:16 AM, Daniel Russel wrote: > >> >> On Nov 1, 2009, at 9:47 AM, Keren Lasker wrote: >> >>> >>>> >>>> >>>> >>>> - helper.create_simplified_by_residue needs to be thought about >>>> since its current method of asigning radii doesn't make sense for >>>> anything other than density based restraints (so it may make >>>> sense to move it to em). >> And, I should add, when you know residue-residue proximities. >> >>>> >>> >>> How else do you propose to define radius other than the particles' >>> sphere cover ? >> radius of gyration or a radius so that the sphere volume matches >> that of the k residues match or something that doesn't go all crazy >> when (depending on the scale) you have beta strands or alpha helices. >> >> Given a molecule interesting geometric aspects include >> 1) residue locations >> 2) regions of space occupied by the molecule >> 3) regions of space free from the protein >> 4) centers of mass >> 5) total volume >> >> Each of these is required for different sorts of restraints. For >> example, EM fitting requires 4 have bounded error, residue >> proximities requires 1 have bounded error, packing a bunch of >> molecules to form a complex requires bounds on 5 be accurate and >> preferable bounds on 2 and 3. >> >> If we are generating a rigid model to approximate a given pdb we >> should be able to get all of them (the helper.create_simplified() >> can be trivially modified to do so, but is slow). Given you >> experience with clustering for finding centers for em-fitting, a >> faster approach might be to cluster the density and then put >> spheres at these cluster centers. We can then measure the error for >> all of the above and increase the number of spheres as needed until >> the error matches the tolerance passed a the parameter to the >> function. >> >> I don't see that doing it along the backbone makes any sense after >> 4ish residues as the set of shapes that those residues occupy can >> vary too much to be represented by a sphere. And if you are holding >> the structure rigid (or only letting it change a bit), you don't >> gain anything from having particles represent consecutive residues >> (and if it is non-rigid, we will have some serious issues with >> preventing it from blowing up). Is there something? >> >> One issue that this raises again is that we use radius for several >> different purposes. >> - for proximity detection, we want to know the maximum extents of >> an object: that is, the size of the space a residue could possibly >> be in >> - for packing we the core set of space that it occupies, which will >> always be smaller than the maximum extent >> >> We could separate the two, but that would be a reasonably >> significant amount of work making sure various classes use the >> right one. But might be worth it. If we do that then >> - restraints that force things to be close together (residue- >> residue proximities for example) could use the extents >> - restraints that force things apart (excluded volume) could use >> the core radius >> >> Then, a simple simplification procedure which >> - uses the cover of the residues to produce an extents radius >> - uses the volume of the residues produce a core radius >> would be pretty OK for most any way one split of the residues. >> Clustering them would still be better than chopping along the >> backbone when coarsening a lot. >> >> Does this make sense? >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev