Hi Matthew, Sorry for this! Sounds boring. To debug this any more I need more information, otherwise this standard error message doesn't tell me much what exactly phenix.refine doesn't like. For example, could you take your ligand molecule from your PDB file and send me so I can simulate the rest of the data and run phenix.refine myself to see exactly what's wrong? Or at least the whole .log file? Thanks! Pavel. Matthew Bowler wrote:
Thanks for all help so far.....
OK, renaming the water to O from O1 worked fine, I also updated CCI Apps, now --do-all works. It only picked out one hetatm though so then I ran elbow naming the residues and it produced cif files for all my ligands - Hooray!
Then I put all these files into the command line with model and structure factors and get:
Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 51 Please edit the PDB file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary (see phenix.refine documentation). Also note that elbow.builder is available to create restraint definitions for unknown ligands.
Again! Even though I now have cif file for all.
Any thoughts greatly appreciated.
BTW refinement without ligands has provided a great map and v.good stats! Really want to refine with ligands though, cheers, Matt.
On 15 Mar 2007, at 19:41, Pavel Afonine wrote:
Hi,
yes, the waters in your file do not match the Monomer Library definition. If you simply replace O1 with O that will fix the problem. For example:
GOOD record: ATOM 22792 O HOH X 1 37.309 34.504 -14.174 1.00 38.28 O
BAD record: ATOM 22792 O1 HOH X 1 37.309 34.504 -14.174 1.00 38.28 O
I have tried running elbow on my pdb already with no luck. using your command I get the error message: elbow.builder: error: no such option: --do-all
That makes me thinking that you are using an old version of CCI Apps or PHENIX. Are you using the latest one? Is the command you run looks like: % elbow.builder x.pdb --do-all
Nigel: do you have any comments?
Pavel.
Matthew Bowler MRC Dunn Human Nutrition Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 2XY Tel: 0044 (0) 1223 252826 Fax: 0044 (0) 1223 252825