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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