Dear colleagues, 

 

I have an issue with the validation website after working with my model in ISOLDE. 

 

More detailed: 

When starting the simulation in ISOLDE, I am running into the error:  

At least one residue in your model does not match any templates in the MD forcefield. This may be due to missing or superfluous atoms, or an unusual residue that has not yet been parametrized. Launching the unparameterized residue widget to help sort this out. 

So certain ligand info is missing (MYR). Then appears the window that allows me to add the information about this ligand and proceed with the refinement. After finishing refinement in ChimeraX/ISOLDE, I loaded the model and the map on https://validate-rcsb-1.wwpdb.org/. But this website showed me the error: 

File upload failed.  Please review the errors below and try again. 

Coordinates issues.  

ERROR: Please remove “TER” card after the single residue “MYR A 1” in line 136 and upload the file again. 

 

Some more observations: 

Although MYR is the first residue in the ChimeraX sequence, it is not visible. 

At the same time, COOT can see it. 

 

 

Please let me know how I can proceed with the https://validate-rcsb-1.wwpdb.org/ after refinement with ISOLDE. 

 

Please let me know if you require a model/map file for the investigation. 

Thank you

 

Kind regards, 

Dmitry