Martin P. Horvath wrote:
I am refining with 1.14 Å data and have included riding hydrogen atoms. In
addition to (and perhaps related to) certain difficulties with real-space
refinement caused by nomenclature mismatch phenix/coot, the alpha-carbon
hydrogen is not removed when deleting an alternate conformation residue. For
each residue previously with two alternate conformations, reduced to one
conformation, the H atom retains A and B tags with partial occupancy. This
is easy to clean up with a text editor, or by running phenix.reduce -trim;
phenix.ready_set, however, if there are plans to smooth out model building
with hydrogens...
OK, I should fix that right away.
As an aside, re: the dictionary in general:
Coot is distributed with a copy of the refmac library, which has PDB
version 2.3 atom names.
You can override that dictionary by setting up CCP4 in the normal way.
You can further override the dictionary by setting the environment
variable COOT_REFMAC_LIB_DIR
So if Phenix distributes a version of the monomer library that has PDB
version 3.x atom names then Coot can use that if you point to it.
Paul.
