Hi Pascal,
I apologize for the delayed reply. Thank you for bringing this to our attention.
Regarding GUI, can you please change the extension of the file to just ".params" instead of ".params.cif"? This "cif" ending may confuse the GUI.
Given that there is no way to have residue id > 9999 in PDB format I assume you are using mmCIF and get something like
Custom bonds:
Sorry: No atom selected: "chain 0 and resname HOH and resid 13322 and name O"
when you try to use your parameters in the command line.
We will work on fixing this issue in the near future.
Meanwhile:
For resids and atom numbers > 9999 Phenix uses hybrid 36 encoding:
Therefore you can try to use this encoding in your parameter file. For example, "resid 13322" will translate to "resid A2KA".
There are several ways to figure out this encoding:
1. Run phenix.cif_as_pdb <your model.cif> and get PDB file where resids will be encoded with hybrid36.
2. if you have python with cctbx library:
from iotbx.pdb.hybrid_36 import hy36encode
hy36encode(width=4, value=13322)
Other option would be splitting chain with > 10k residues into several chains with less than 10k residues.
Best regards,
Oleg Sobolev.