[phenixbb] Updating other tools to use and output in mmCIF format and option to add hydrogens in real_space_refine

[Nigel Moriarty]

Adrian

Pavel comments are correct. I can add that I have spent most of this week
getting the "ReadySet!-for-mmCIF" working. I am hoping for a release in the
near future.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Email : NWMoriarty at LBL.gov
Web  : CCI.LBL.gov
ORCID : orcid.org/0000-0001-8857-9464


On Tue, Sep 19, 2023 at 7:12 PM Pavel Afonine <pafonine at lbl.gov> wrote:

> Hi Adrian,
>
> thanks for suggestions and comments.
>
> I hope Nigel can comment more, AFAIK making ReadySet mmCIF friendly is
> an on-going project and perhaps that won't happen before the upcoming
> release.
>
> The troubles you describe look a bit artificial to me. Here is why.
> First, mmCIF is now the only file format accepted by PDB for
> crystallographic depositions and AFAIK the same is about to happen for
> cryo-EM (if not happened already). So it may be a good idea to use mmCIF
> consistently. Second, adding H atoms seems more like a model building
> rather than refinement, so while it is possible of course to add them as
> part of a refinement run, it doesn't seem to be a huge deal adding them
> to your model once (once you are ready) and then keep from that point
> on. And, finally, it's been said here and elsewhere countless amount of
> times that adding H for refinement and then deleting them afterwards is
> not a good practice (to say the least).
>
> All the best!
> Pavel
>
> On 9/14/23 06:18, Adrián González López wrote:
> > Hi Phenix team,
> >
> > I have a couple of feature suggestions:
> > It would be great if all the other tools within phenix would be able to
> have mmCIF files as both input and output. It causes a lot of problems when
> you are forced to switch between pdb and mmCIF, for example when using
> ReadySet to add hydrogens. On that note, it would also be very useful to
> have an option in real space refine to add hydrogens automatically before
> the refinement and remove them after the refinement.
> >
> > Thanks!
> >
> > Best,
> > Adrián
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