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 : [email protected] Web : CCI.LBL.gov ORCID : orcid.org/0000-0001-8857-9464 On Mon, Nov 27, 2023 at 4:38 AM Xavier Brazzolotto 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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]