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How about LSQMAN ? with ATOM_types Side_chain ? That should do the trick. Jürgen P.S. sorry it's not really a CCP4 related program, but I use it very frequently in conjunction with the CCP4 suite :-) On Feb 26, 2010, at 11:22 AM, Ed Pozharski wrote: > On Fri, 2010-02-26 at 16:50 +0100, Gerard DVD Kleywegt wrote: >> But it still won't solve Miri's problem. I think what she is asking >> for is a >> program that detects which atoms should be matched to which, >> irrespective of >> their names (i.e., not assuming they are called " CA ") and order >> (i.e., not >> nicely sequential such as amino-acid residues), and then applies the >> operator >> that follows from that. >> >> > > How about FM option in molrep? > http://www.msg.ucsf.edu/local/programs/ccp4-6.0.2/html/molrep.html#FM > > Other MR programs can be used as well, just generate FC from one model > in a suitable cell and run search with another. > > HTH, > > Ed. > > -- > Edwin Pozharski, PhD, Assistant Professor > University of Maryland, Baltimore > ---------------------------------------------- > When the Way is forgotten duty and justice appear; > Then knowledge and wisdom are born along with hypocrisy. > When harmonious relationships dissolve then respect and devotion > arise; > When a nation falls to chaos then loyalty and patriotism are born. > ------------------------------ / Lao Tse / - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/