Hi Firdous,
Can you please update to 1.19.2 version of Phenix here:
https://www.phenix-online.org/download/
and confirm that the problem still exists? If so, can you please share the
files or point me to publicly available databases?
Best regards,
Oleg Sobolev.
On Mon, Jul 26, 2021 at 12:51 AM Firdous Tarique
Hi
I am getting the following error during real space refinement of the model and map. Can anybody suggest what it is actually about. It is something about geometry_restraints but I am not able to figure it out where.
Can we do something in refinement settings Or change any threshold value to avoid these problems?
Input is 80S.pdb ribosome and its corresponding em map.
File "/apps/PHENIX/1.18.2/phenix-1.18.2-3874/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1486, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels)
File "/apps/PHENIX/1.18.2/phenix-1.18.2-3874/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1388, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac)
File "/apps/PHENIX/1.18.2/phenix-1.18.2-3874/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1269, in check_bonded_distance_cutoff raise RuntimeError(msg)
Best regards
Firdous _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]