[phenixbb] pdb waters

Matthew Bowler mwb at mrc-dunn.cam.ac.uk
Fri Mar 16 08:03:22 PDT 2007

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

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