Sorry I meant to ask if there was any way to use phenix.ready_set "old". I don't know the syntax but I read that it would output hydgrogens with a nomenclature that was compatable with coot library.
Thanks -Yarrow hello,
After reading many posts on the phenix and coot boards I realize that the hydrogens produced by phenix.ready_set are not compatable with coot. Specifically, coot does not recognize HB3 and HD3 hydrogens. When I do realspace refinement they fly off into space. I have edited HB3 to read HB2 and HB2 to read HB1 and everything works well.
I was wondering if there is a fix for this besides editing the pdb each time you run phenix.ready_set.
Is there a way to add HB3 hydrogens to the phenix library (CCP4 library)?
Thank you
-Yarrow
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