Re: [phenixbb] how to get rid of the H added by Phenix ready_set

On Wed, Jan 25, 2012 at 1:27 PM, Dialing Pretty wrote:

Will you please tell me a software to get rid of the H added by Phenix ready_set?

phenix.reduce -Trim model.pdb > model_noH.pdb or 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 model alone. -Nat