[phenixbb] Bug squash request

Nathaniel Echols nechols at lbl.gov
Thu Jan 17 15:11:38 PST 2013

On Thu, Jan 17, 2013 at 7:17 AM, Antony Oliver
<Antony.Oliver at sussex.ac.uk> wrote:
> I've noticed a slightly annoying "feature" when using a reference model to help in refinement of  low-resolution structures.
> phenix.refine seems to take it's crystal parameters and space-group from whichever PDB was loaded last, even after setting one PDB as the "reference model" and the other as the "Input model".


> When running phenix.refine it gives you a nice error message telling you that the space group information is incorrect, and that you may have used the reference model's parameters by mistake…
> But surely, it should just (by default) only take (check?) the cell parameters and space group information from the "Input PDB"?

I agree that this is not well-designed - the problem however is that
you can have multiple input PDB files, e.g. one for protein, one for
ligand, etc.  When a PDB file is added it isn't immediately obvious
what its purpose is, but the assumption is that if it has symmetry, we
want to use that information.  It used to only pull information from
the first file, but I received multiple complaints about this.  I may
be able to figure out something smarter, but it's not trivial.  (One
option would be to pop up a message asking if you want to use the
symmetry, in the case where it is already defined from a previously
loaded file, but I personally find pop-up messages annoying.)  For now
I will add a button that will let you choose which file to pull the
symmetry from, so you can easily revert to the correct parameters.


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