9 Feb
2012
9 Feb
'12
4:05 p.m.
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