Hi, a workaround for this special case at the moment is to use after ready set the pdbtools to remove the wrongly placed atoms. phenix.pdbtools file.pdb remove="name HO4" Or remove whatever atom should be removed. Its a bit more work for the moment, but it works well for me Am Freitag 10 Februar 2012 01:05:49 schrieb Jianghai Zhu:
Hi,
I am using phenix.ready_set (version 1.7.3) to add hydrogens to my structure. I found out that it makes a few mistakes when dealing with glycans. It adds hydrogens to C1, O4, O3, O6 even when these atoms have formed covalent bonds with other sugars and residues. Subsequent phenix.refine aborts because of these incorrect hydrogens. However, when I use phenix.reduce directly, all hydrogens are placed correctly. I assume something went wrong in phenix.ready_set. The problem with phenix.reduce is that it doesn't know how to deal with ligand whereas phenix.ready_set does when a cif file is provided.
-- Jianghai
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