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
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