Jianghai
Its true that ReadySet! does not handle the glycans as well as it
should. Its on my list of things to fix, but you can delete the
hydrogens by hand for a short time. This actually brings up an
interesting point. I believe its better to add the hydrogens once and
use that model for all subsequent refinements. In this scenario, you
use ReadySet! once and the addition of hydrogens is a "checkpoint" in
the refinement process.
Nigel
On Thu, Feb 9, 2012 at 4:05 PM, 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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