Hi Yi Min,

 

my problem number 2 was indeed resolved after I restarted my system.

 

Thank you,

Andrea



On Tuesday, July 09, 2024 14:47 CEST, Yi Min Ng <[email protected]> wrote:

 

Hi Andrea,

 
I am still new to this field and I have previously came across your #2 problem when trying to generate Table 1 using Phenix. I don't  know exactly what was causing the problem but I somehow managed to generate Table 1 after restarting the GUI. You might want to try restarting the software if you haven't tried so?

 
Hope some experts will be able to help you with the problems soon 🤞

 
Best wishes,
Yi Min
 

From: [email protected] <[email protected]> on behalf of Andrea Smith <[email protected]>
Sent: 09 July 2024 14:25
To: [email protected] <[email protected]>
Subject: [phenixbb] refine and Table 1

 

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.