NUDT7A Copy atoms for second ligand and process to histogram

[nelse003]

Created branch for this: copy_NUDT7_atoms

[nelse003]

I'm trying to refine multiple copies of the same ligand in refmac. I've tried following previous advice:

For refmac to refine a structure with two or more ligands, the individual cif files have to be merged into one file.

You can do that with a VERY archaic program called LIBCHECK from CCP4.

LIBCHECK <<eof _DOC N _FILE_L file1.cif _FILE_L2 file2.cif _FILE_O out_prefix _END eof

which will create a file called out_prefix.lib, which you can rename to out_prefix.cif.

https://github.com/xchem/XChemExplorer/issues/49

This method does generate a cif file which can be given to refmac (I am using the pandda.quick_refine wrapper to refmac). The below command should give you all required filepaths to run this:

giant.quick_refine input.pdb=/dls/science/groups/i04-1/elliot-dev/Work/exhaustive_search/NUDT7_Copied_atoms/NUDT7A-x1787/multi-state-model.pdb input.mtz=/dls/science/groups/i04-1/elliot-dev/Work/exhaustive_search/NUDT7_Copied_atoms/NUDT7A-x1787/NUDT7A-x1787.free.mtz input.cif=/dls/science/groups/i04-1/elliot-dev/Work/exhaustive_search/NUDT7_Copied_atoms/NUDT7A-x1787/OX-210_two_copies.cif params=/dls/science/groups/i04-1/elliot-dev/Work/exhaustive_search/NUDT7_Copied_atoms/NUDT7A-x1787/multi-state-restraints.refmac.params

It fails in refmac, due to the multiple ligands.

[nelse003]

Discuss with Tobias on 28/02/18

[nelse003]

This is not related to requiring two copies in the cif: the cif was not being copied correctly. Also the order of the atoms in the pdb file differed between the ligands initially. this was changed by copying the coordinates of both ligands from NUDT7A-x0299. These now refine.

[nelse003]

Occupancy plot generated. Refinements and occupancy code @ /dls/science/groups/i04-1/elliot-dev/Work/exhaustive_search/NUDT7_Copied_atoms