I'm attempting to perform atomistic optimal structure alignment on an inorganic species. Can anyone point me in the right direction to software or a technique for performing this?
There exists a wide range of structural alignment software, but this really appears to be geared towards aligning protein backbones, whereas I'm interested in aligning unlabelled Cartesian coordinates of small molecules.
Inorganic structures – that could be proper solid or molecular metalloorgnic. For the later one you can use xp (program written G.M.Shedrick - comes with Bruker diffractometers). If you have running license of Cambridge Crystal Data Base there is program called IsoStar, and I think that it should do the job. I haven't used it my self but apparently Olex2 can make aligning of fragments (this program is free so that's the place were you can start). I'm not quite sure but I think that old GROMOS code could also make a fit of orthogonal coordinates.
I'm sure VMD (although also geared towards protein alignment) is flexible enough to align any two sets of atoms. You will almost definitely have to learn some TCL scripting, but getting past the (perhaps steep) learning curve is well worth the effort. Besides VMD has excellent documentation. If you post a more specific problem I'll be happy to post a more specific answer:)
