[phenixbb] Error 1.21rc1-5156 macOS and cross special position

[Nigel Moriarty]

Xavier

Can you send the inputs to Pavel and I directly?

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 Mon, Nov 27, 2023 at 4:38 AM Xavier Brazzolotto <xbrazzolotto at gmail.com>
wrote:

> Dear Phenix developers,
>
> I have recently updated to macOS Sonoma and updated Phenix to the latest
> RC (1.21rc1-5156).
>
> I do have recent data where a residue gets a bit too close to its
> symmetric mate.
> In order to be able to start the refinement, I have to select the model
> interpretation option « allow_polymer_cross_special_position=True »
> In this case, the refinement process starts and does my 3 refinement
> cycles.
>
> However, the UI gives me a final error message stating that I have to
> enable the « cross-special position » (which is already True).
> The refined data are present (pdb, mtz, log, cif, eff, geo) but I do not
> get any analysis on these data. No _info.txt, no .kin files.
> The log ends with a « Sorry »
>
> If I deliberately move the faulty residue a bit out of its position (no
> more clashing with its symmetric mate) and NOT allow the cross-special
> position, then the refinement ends well with the correct final data
> analysis.
>
> Not a big deal per se, but but I suspect a small issue in the initiation
> of the analysis programs (Molprobity / King / etc…).
>
> Xavier
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