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

Jovine Luca luca.jovine at ki.se
Tue Aug 24 06:12:40 PDT 2010

On Aug 23, 2010, at 9:09 PM, 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

This is indeed what we have also been doing, and I can confirm that it appears to work just fine!

Best, Luca

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