Refinement failure of bound and ground states

[nelse003]

Raised by Romain Talon

I don’t know who has time for this now Elliot moved on but the export script is failing to create the output.ground-state.pdb and split.ground-state.pdb files after the refinement cycle.
You can see an example here: /dls/labxchem/data/2018/lb18145-104/processing/analysis/initial_model/LC_TbrB1-x0140
The symlink are generated but not the files.

Is there a workaround to regenerate this files?

[nelse003]

Romain suggested working on NUDT22 Visit instead, as the issue would be clearer:

/dls/labxchem/data/2016/lb13385-46/processing/analysis/initial_model/

Many datasets have both ground and bound states. i.e

lrwxrwxrwx. 1 mlk83353 mlk83353 42 Oct 30 15:31 NUDT22A-x1076/refine.split.bound-state.pdb -> Refine_0001/refine_1.split.bound-state.pdb
lrwxrwxrwx. 1 mlk83353 mlk83353 43 Oct 30 15:31 NUDT22A-x1076/refine.split.ground-state.pdb -> Refine_0001/refine_1.split.ground-state.pdb

However some fail to produce bound states:

lrwxrwxrwx. 1 mlk83353 mlk83353 42 Oct 30 15:31 NUDT22A-x1391/refine.split.bound-state.pdb -> Refine_0002/refine_2.split.bound-state.pdb (SYMLINK ONLY)
lrwxrwxrwx. 1 mlk83353 mlk83353 43 Oct 30 15:31 NUDT22A-x1391/refine.split.ground-state.pdb -> Refine_0002/refine_2.split.ground-state.pdb

[nelse003]

In a failed case there is an existing refinement:

drwxrwx---+ 3 mlk83353 mlk83353 4096 Jun 3 16:27 Refine_0001
drwxrwx---+ 3 mlk83353 mlk83353 4096 Oct 30 15:31 Refine_0002

[nelse003]

In

/dls/labxchem/data/2016/lb13385-46/processing/analysis/panddas/processed_datasets/NUDT22A-x1391/modelled_structures

-rw-rw----+ 1 mlk83353 mlk83353 205015 May 1 2019 fitted-v0001.pdb
lrwxrwxrwx. 1 mlk83353 mlk83353 16 May 1 2019 NUDT22A-x1391-pandda-model.pdb -> fitted-v0001.pdb

whereas in other cases these are done in may,

[nelse003]

Romain wants to retry clearing the folder and will update when done