[phenixbb] how to get rid of the H added by Phenix ready_set
nechols at lbl.gov
Wed Jan 25 13:33:03 PST 2012
On Wed, Jan 25, 2012 at 1:27 PM, Dialing Pretty <hdc123hdc123 at yahoo.com> wrote:
> Will you please tell me a software to get rid of the H added by Phenix
phenix.reduce -Trim model.pdb > model_noH.pdb
phenix.pdbtools model.pdb remove="element H or element D"
> For Phenix refine I have used the H added PDB by ready_set. Although there
> is the opinion on that for RCSB depositation added H is fine, but there is
> also the opinion for RCSB depositation added H is not necessary. Thus I need
> to know how to remove the added H.
You don't necessarily need to do anything specifically to deal with
the RCSB - they may remove the hydrogens automatically (whether you
want them to or not). But our opinion is that you should leave the
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