Hi Bala, Chimera fitting does rigid body rotation and translation to optimize the correlation of a map simulated from your molecular model to the EM map. Once you've done that there is no further "refinement" that Chimera can do. It does not have any flexible fitting methods. You can however get different fits by using different fitting parameters in Chimera and it is rarely clear which set of parameters is best. You can vary the region of the EM map that is used by changing the contour level. Only data above the displayed contour level is used. You can change the simulated resolution for you molecular model. Another "refinement" to the fit is to take into account clashes with neighboring models. That can be done with the "fit" command symmetric fitting option (if the map has symmetry) or sequential fitting option if you have more than one molecular model fit into an asymmetric map. Video examples of the different types of fitting are on the Chimera video tutorials web page. http://www.cgl.ucsf.edu/chimera/videodoc/videodoc.html To use other programs to do say flexible fitting you would write out your initial fit done in Chimera with File / Save PDB... and make sure to check the "save relative to" option and choose the map you were fitting into. This saves the PDB in its new position in the coordinate system of the map. That way other software loading that PDB will place it in the location you found by fitting in Chimera. Tom
Friends, I used "fit" command to fit a structure onto a EM map and obtained a list of fits. Now i want to choose the best fit and refine it further. I would like to know if there is any way to refine a fit produced by fit command in Chimera. Or can i use any other software for the same, which can take chimera's fit as input and refine it further.
Thanks, Bala
-- C. Balasubramanian