[phenixbb] phenix.ready_set hydrogens not compatable with coot library

Phil Evans pre at mrc-lmb.cam.ac.uk
Mon Aug 23 13:08:03 PDT 2010

Coming from using Refmac I'm slightly puzzled by the philosophy here. By  default (I believe) Refmac always adds riding hydrogens for the refinement but doesn't output them in the refined PDB files. This seems to me to be the right thing to do. I don't see any reason for not including Hs in refinement since you know where most of them are relative to the heavy atoms, and they will (maybe marginally) improve things. On the other hand I don't normally want them cluttering up the display in Coot (maybe because I'm just not used to them), and I certainly don't want to include them in my PDB deposition, since I don't think they are an independent part of the model, and including them would imply I can see them. They are I suppose useful in bump checks, but I would just add them back for that purpose


On 23 Aug 2010, at 20:09, Joseph Noel wrote:

> Hi All,
> Indeed even the latest COOT still relies on the old PDB format and hydrogens fly. Its probably not prudent to use hydrogens in refinement then remove them and add back each time. Kind of defeats the purpose of using them in the first place. Until COOT is updated I found a pretty easy way around things as long as you have access to the internet. Just use the MOLPROBITY site (http://molprobity.biochem.duke.edu/). In addition to it being a fantastic tool for really cleaning up structures, you can quickly upload your refined file from Phenix with hydrogens, then hit the button to downgrade to PDB v23. It creates the appropriate file with renamed hydrogens that work great in COOT. You can then re-upload the COOT rebuilt model and it will "upgrade" naming to the latest PDB version. Download that file and there you go for Phenix refinement. Sounds like a bit but very fast and easy to implement until COOT is upgraded.
> Joe
> ___________________________________________________________
> Joseph P. Noel, Ph.D.
> Investigator, Howard Hughes Medical Institute
> Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics
> The Salk Institute for Biological Studies
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