Hi Andy, I have not tried this but here are my ideas. First when you open the bead model (PDB file) it will probably look crazy because Chimera is trying to treat the bead model as a molecule when really it is just a grid of points. It may try to draw a ribbon through it. So hide the ribbon and show the atoms as spheres using menu entries Actions / Ribbon / hide Actions / Atom / show Actions / Atom / sphere or equivalent commands ~ribbon display repr sphere To fit a molecule into the bead model I suggest turning the bead model into a density map using the molmap command. For example, if the bead model is #0, make a 20 Angstrom resolution map with molmap #0 20 This just puts a Gaussian at each bead position to make a density map. Then place the molecule into this map in the suspected position by hand and locally optimize that fit with the Fit-in-Map tool. http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#fitmode... A new Chimera feature in Chimera daily builds computes theoretical SAX profiles for a PDB model and plots them against experimental profiles. Tools / Higher-Order Structure / Small-Angle X-ray Profile It uses a web service hosted at our lab to compute the profile. It isn't yet documented (added just a few weeks ago). Tom

Chimera Team & users, We have been using SAXS data and the DAMMIN software from the Svergun group. The bead model that DAMMIN produces approximates the shape and volume of the molecule. If one has a three dimensional structure of the molecule, then it becomes valuable to do a best superposition of the structure into the bead-model shape. Chimera is our preferred molecular display & analysis software, and we would like to perform this fitting in Chimera. Do you have any experience in how to display the bead-model output of DAMMIN and to fit or superimpose the bead model with a known structure?

Thanks Andy Byrd