[phenixbb] pdb waters

[Pavel Afonine]

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
>