[phenixbb] refinement with a covalent inhibitor.

[Maia Cherney]

Hi Nigel,
I installed the phenix version 1.4-4 and now I get this error when
running phenix.elbow model.pdb --do-all
> Traceback (most recent call last):
>   File 
> "/raid/programs/linux/phenix-1.4-4/elbow/elbow/command_line/builder.py", 
> line 1273, in <module>
>     run()
>   File 
> "/raid/programs/linux/phenix-1.4-4/elbow/elbow/command_line/builder.py", 
> line 1126, in run
>     molecule = builder(molecule, options)
>   File 
> "/raid/programs/linux/phenix-1.4-4/elbow/elbow/command_line/builder.py", 
> line 467, in builder
>     verbose=(not options.silent),
>   File 
> "/raid/programs/linux/phenix-1.4-4/elbow/elbow/chemistry/BondTopologyMixins.py", 
> line 188, in Bondise
>     self.CheckBondOrderWithoutHydrogens()
>   File 
> "/raid/programs/linux/phenix-1.4-4/elbow/elbow/chemistry/BondTopologyMixins.py", 
> line 1038, in CheckBondOrderWithoutHydrogens
>     self.FlattenCNN()
>   File 
> "/raid/programs/linux/phenix-1.4-4/elbow/elbow/chemistry/TopologyMixins.py", 
> line 1741, in FlattenCNN
>     rc = self.FlattenCNNOther(set_restraint_class=set_restraint_class)
>   File 
> "/raid/programs/linux/phenix-1.4-4/elbow/elbow/chemistry/TopologyMixins.py", 
> line 1799, in FlattenCNNOther
>     planes = self._cnn_planar_group(carbon, nitrogens)
> NameError: global name 'carbon' is not defined

Maia




Nigel W Moriarty wrote:
> Maia
>
> Using PHENIX 1.4-4 and 1.4-6, eLBOW generates a CIF with 4 planar 
> groups including the carboxyl group missing from the earlier PHENIX 
> version I believe you used.  I have attached it.  There are a few 
> other things I should mention.
>
> I used a tool called ReadySet!
>
> phenix.ready_set model.pdb
>
> which will generate (using eLBOW) CIF files for all the ligands in the 
> model using the data from the Chemical Components database from the 
> PDB.  I would recommend that you use ReadySet! for preparing a PDB 
> file for refinement.  It also adds hydrogens to your model which is 
> usually a good thing.
>
> Your example does have some nuances.  You mention that it is 
> covalently bound to the CYS.  I have attached the two additional files 
> needed to inform phenix.refine of the covalent bond.  I used eLBOW 
> directly for this but will ensure that ReadySet! will do the same 
> function in the next release.
>
> An additional function that I have been working on recently is the 
> removal of the hydrogen in a carboxyl group when the ligand is in the 
> model.  I shall have that in the next PHENIX release.
>
> Finally, I did a refinement using dummy reflection data and the 
> carboxyl group remained planar.
>
> If you have any problems with any of the files, feel free to contact 
> me directly.
>
> Nigel
>
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