[phenixbb] phenix.ready_set hydrogens not compatable with coot library

amadrona at uci.edu amadrona at uci.edu
Sat Aug 21 17:41:59 PDT 2010

> 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.



> 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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