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