If I understand your question correctly, you have a couple of atoms which you could align to get the rotation & translation then you can use these values with maprot (CCP4) or mama (USF) to actually superimpose maps.
Jürgen On Mar 21, 2013, at 11:29 PM, Chen Zhao wrote: Dear all, Does anybody know some softwares for aligning electron density maps? I tried transforming map by SQL model fit extension in COOT, which turned out to be not working: the map it transformed is the one supposed to be fixed. If I switch the moving model with the reference model, I only got some error messages. I also tried the "Superpose maps" utility in PHENIX, however, since they are nucleic acid structures, it seems that the sequences cannot be recognized. Thank you very much! Best, Chen ...................... Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu
