Hi everyone,

1. I have an issue with phenix.refine being unable to open generated pdb and mtz files in coot after refinement. It claims “ERROR: refinement output file not found!” This started happening after I opened the model in ChimeraX and used dssp command and then saved model as pdb that I used for further refinements. The files generated from phenix.refine actually exist, but instead of just being named e.g. myprotein_refine20.pdb they are called myprotein_refine19_refine020.pdb (yes there is an extra refine and an extra 0). This has never happened to me before.
2. I am also trying to generate "Table 1" for journal. I input my pdb into model file and mtz into reflection file. When I click Run, I get an error message:
   "a model is referenced in the phil which is not in the data manager". What does this mean?
3. I also tried to validate my model using pdb validate server, but when I upload cif files generated as output from phenix.refine, the server shows “Error processing uploaded files…Click to reload”. (However, when I use the Get PDB validation report task in phenix, I get a validation report pdf with no issues.)

Is all of this caused by the changes the ChimeraX's dssp command did to my pdb?

Thank you,

Andrea

Running Phenix 1.21-5207 from GUI on Ubuntu 20.04.3.