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 Andrea Can you send the model to me directly? On Tue, Jul 9, 2024 at 5:29 AM Andrea Smith wrote:

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. _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]