Ethan A Merritt wrote: > On Tuesday 04 July 2006 11:46 am, you wrote: >> I'm looking for a tool that can essentially factor out anisotropic B >> factors to larger-scale motion like TLS. But I'd like to also end up >> with the residual anisotropic B, so I could examine what local motion >> remains after removing the effects of larger-scale movement. > > I'm afraid I don't understand what you are trying to do. > Could you explain, giving equations or examples? > Even better, could you explain what you are trying to accomplish?
I'm starting with an anisotropically refined protein. The problem is that for each atom, the anisotropic B is a combination of many different scales of motion, from global or domain-level to very local. I would like to be able to separate these levels by first "factoring out" motions common to _all_ atoms from the single-atom anisotropic B's into larger TLS groups, then motions common to large domains, and so forth. This would define different layers or shells of TLS domains -- a global domain for global movements, then within that, various sub-domains for smaller-scale movements, and so forth. The "leftover" or residual anisotropic B would be highly local and would have no global or large-scale motion effects still contributing to it. >> Does anyone know of some way to do this? I looked at the TLSMD server, >> but it didn't seem to do exactly what I want. > > The mmLib package and the TLSMD code can probably do what you > want, even if it isn't one of the default output modes of the > server. But I can't offer any more help until I understand better > what you are aiming for. I hope I've clarified what I want. I've just started using pymmlib recently for some other work and it's saved me many hours, so I would be happy to use it again. Thanks, Donnie
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