[phenixbb] links in phenix

Nathaniel Echols nechols at lbl.gov
Wed Jan 25 07:26:05 PST 2012

On Wed, Jan 25, 2012 at 2:31 AM, Christian Roth
<christian.roth at bbz.uni-leipzig.de> wrote:
> Somehow the old restraits are already in the .eff file and the new ones are
> ignored how I could I avoid this. Simply closing the GUI an reopening?

Yes, and I'll fix that ASAP today... (sigh)

> A last question regarding the hydrogens in refinement. For rebuilding it is
> nice to remove the hydrogens. Normally I use the commandline for this purpose.
> But It would be nice to do it automatically after refinement as a third pdb
> output in addition to the two standard outputs phenix_output.pdb and the
> phenix_output_reduce.pdb. Is there an option in the GUI to do this
> automatically. I thought I have seen this previously but cannot find it anymore

You're not the first person to ask for this, but I think we decided
that we wanted to discourage people from depositing PDB files that had
been modified post-refinement.  However, since the PDB annotators
often (usually? always?) do this anyway, we may be waging a futile


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