[phenixbb] Problem in real space

[Oleg Sobolev]

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 <kahkashantarique at gmail.com>
wrote:

> 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
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