On 17 Aug 2011, at 17:10, Eric Karg wrote: > Thanks for the suggestions. I could solve the problem by using the setenv > command to the coot directory,but I still cannot use the Real Space Refine > Zone in Coot because the names are not compatible. I'm trying to build an RNA > molecule by the way.
Having recently had exactly the same problem this sounds like you have the wrong dictionary in coot as well. If at start-up you don't get a line like: There are 2 data in /sw64/share/coot/lib/data/monomers/u/U.cif but instead get There are 2 data in /sw64/share/coot/lib/data/monomers/u/UR.cif Then you need to get the new dictionary from http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_experimental/refmac_dictionary_v5.29.tar.gz extract it and use that to replace /path/to/coot/lib/data/monomers It seems like some of the distributed coot builds have the old dictionary (The OS X fink one definitely does because coot.info downloads http://www.ysbl.york.ac.uk/refmac/data/refmac_dictionary.tar.gz) and that breaks refinement for nucleic acid. Hope that helps, Huw -- Dr Huw Jenkins Astbury Centre for Structural Molecular Biology University of Leeds
